Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Carlos-Francisco Méndez-Cruz
4e4ff446 1 parent 3f696776

Conditions tagged per XML file - csv format

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Showing 26 changed files with 2875 additions and 2107 deletions
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
3 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
4 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
5 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
2 "GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 6 "GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 "GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 7 "GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 "GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 8 "GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
...@@ -14,10 +18,6 @@ ...@@ -14,10 +18,6 @@
14 "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 18 "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
15 "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 19 "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
16 "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 20 "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
17 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
18 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
19 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
20 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
21 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 21 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
22 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 22 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
23 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 23 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
3 +"GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
4 +"GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
5 +"GSE41186","GSM1010202","ß - Anaerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
6 +"GSE41186","GSM1010203","ß - Anaerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
7 +"GSE41186","GSM1010204","ß - Aerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
8 +"GSE41186","GSM1010205","ß - Aerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
9 +"GSE41186","GSM1010206","HNS - Anaerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
10 +"GSE41186","GSM1010207","HNS - Aerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
11 +"GSE41186","GSM1010208","IHF - Anaerobic A","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
12 +"GSE41186","GSM1010209","∆fnr - Anaeroibc","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","∆fnr, PK4854","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
13 +"GSE41186","GSM1010210","Ptac::fnr - A - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
14 +"GSE41186","GSM1010211","Ptac::fnr - B - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
15 +"GSE41186","GSM1010212","Ptac::fnr - A - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
16 +"GSE41186","GSM1010213","Ptac::fnr - B - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
17 +"GSE41186","GSM1010214","Ptac::fnr - A - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
18 +"GSE41186","GSM1010215","Ptac::fnr - B - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
19 +"GSE41186","GSM1010216","Ptac::fnr - C - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
20 +"GSE41186","GSM1010217","FNR - Anaerobic - Affinity Purified - A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
21 +"GSE41186","GSM1010218","FNR - Anaerobic - Affinity Purified - B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
22 +"GSE41186","GSM1054383","FNR - ∆hns∆stpA A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
23 +"GSE41186","GSM1054384","FNR - ∆hns∆stpA B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
24 +"GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
25 +"GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
26 +"GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
27 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
28 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
29 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
30 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
2 "GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 31 "GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 "GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 32 "GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 "GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 33 "GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
...@@ -14,10 +43,6 @@ ...@@ -14,10 +43,6 @@
14 "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 43 "GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
15 "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 44 "GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
16 "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 45 "GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
17 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
18 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
19 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
20 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
21 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 46 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
22 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 47 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
23 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 48 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
...@@ -33,28 +58,3 @@ ...@@ -33,28 +58,3 @@
33 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 58 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
34 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 59 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
35 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask","" 60 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
36 -"GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
37 -"GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
38 -"GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
39 -"GSE41186","GSM1010202","ß - Anaerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
40 -"GSE41186","GSM1010203","ß - Anaerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
41 -"GSE41186","GSM1010204","ß - Aerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
42 -"GSE41186","GSM1010205","ß - Aerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
43 -"GSE41186","GSM1010206","HNS - Anaerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
44 -"GSE41186","GSM1010207","HNS - Aerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
45 -"GSE41186","GSM1010208","IHF - Anaerobic A","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
46 -"GSE41186","GSM1010209","∆fnr - Anaeroibc","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","∆fnr, PK4854","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
47 -"GSE41186","GSM1010210","Ptac::fnr - A - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
48 -"GSE41186","GSM1010211","Ptac::fnr - B - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
49 -"GSE41186","GSM1010212","Ptac::fnr - A - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
50 -"GSE41186","GSM1010213","Ptac::fnr - B - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
51 -"GSE41186","GSM1010214","Ptac::fnr - A - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
52 -"GSE41186","GSM1010215","Ptac::fnr - B - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
53 -"GSE41186","GSM1010216","Ptac::fnr - C - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
54 -"GSE41186","GSM1010217","FNR - Anaerobic - Affinity Purified - A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
55 -"GSE41186","GSM1010218","FNR - Anaerobic - Affinity Purified - B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
56 -"GSE41186","GSM1054383","FNR - ∆hns∆stpA A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
57 -"GSE41186","GSM1054384","FNR - ∆hns∆stpA B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
58 -"GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
59 -"GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
60 -"GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
2 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 5 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
3 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 6 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
4 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 7 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
5 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 8 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
6 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
7 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
8 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
9 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
10 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
11 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
12 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
13 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
14 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
15 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
16 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
17 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
18 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
19 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
20 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
21 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
22 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
23 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
24 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
25 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 9 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
26 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 10 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
27 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 11 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -47,6 +31,22 @@ ...@@ -47,6 +31,22 @@
47 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 31 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
48 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 32 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
49 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 33 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
34 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
35 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
36 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
37 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
38 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
39 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
40 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
41 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
42 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
43 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
44 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
45 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
46 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
47 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
48 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
49 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
50 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 50 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
51 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 51 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
52 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 52 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
2 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 5 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
3 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 6 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
4 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 7 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
...@@ -51,25 +54,6 @@ ...@@ -51,25 +54,6 @@
51 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 54 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
52 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 55 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
53 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 56 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
54 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
55 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
56 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
57 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
58 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
60 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
62 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
68 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
70 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
71 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
72 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
73 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 57 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
74 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 58 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
75 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 59 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -95,6 +79,22 @@ ...@@ -95,6 +79,22 @@
95 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 79 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
96 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 80 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
97 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 81 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
82 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
83 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
84 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
85 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
86 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
87 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
88 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
89 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
90 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
91 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
92 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
93 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
94 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
95 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
96 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
97 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
98 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 98 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
99 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 99 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
100 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 100 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
3 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
4 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
5 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
6 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
7 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
8 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
9 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
10 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
11 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
12 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
13 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
14 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
15 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
16 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
17 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
18 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
19 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
20 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
2 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 21 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
3 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 22 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
4 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 23 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
...@@ -51,25 +70,6 @@ ...@@ -51,25 +70,6 @@
51 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 70 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
52 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 71 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
53 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 72 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
54 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
55 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
56 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
57 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
58 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
60 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
62 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
68 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
70 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
71 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
72 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
73 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 73 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
74 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 74 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
75 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 75 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -95,22 +95,22 @@ ...@@ -95,22 +95,22 @@
95 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 95 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
96 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 96 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
97 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 97 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
98 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 98 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
99 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 99 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
100 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 100 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
101 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 101 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
102 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 102 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
103 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 103 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
104 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 104 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
105 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 105 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
106 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 106 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
107 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 107 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
108 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 108 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
109 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 109 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
110 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 110 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
111 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 111 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
112 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 112 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
113 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 113 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
114 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 114 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
115 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 115 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
116 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 116 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
3 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
4 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
5 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
6 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
7 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
8 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
9 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
10 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
11 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
12 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
13 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
14 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
15 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
16 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
17 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
18 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
19 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
20 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
21 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
22 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
23 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
24 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
25 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
26 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
27 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
28 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
29 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
30 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
31 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
32 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
2 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 33 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
3 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 34 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
4 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 35 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
...@@ -51,25 +82,6 @@ ...@@ -51,25 +82,6 @@
51 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 82 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
52 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 83 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
53 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 84 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
54 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
55 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
56 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
57 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
58 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
60 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
62 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
68 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
70 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
71 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
72 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
73 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 85 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
74 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 86 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
75 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 87 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -95,22 +107,22 @@ ...@@ -95,22 +107,22 @@
95 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 107 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
96 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 108 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
97 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 109 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
98 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 110 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
99 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 111 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
100 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 112 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
101 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 113 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
102 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 114 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
103 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 115 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
104 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 116 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
105 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 117 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
106 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 118 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
107 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 119 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
108 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 120 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
109 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 121 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
110 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 122 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
111 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 123 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
112 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 124 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
113 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 125 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
114 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 126 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
115 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 127 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
116 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 128 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
...@@ -126,15 +138,3 @@ ...@@ -126,15 +138,3 @@
126 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 138 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
127 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 139 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
128 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask","" 140 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
129 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
130 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
131 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
132 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
133 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
134 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
135 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
136 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
137 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
138 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
139 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
140 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
3 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
4 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
5 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
6 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
7 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
8 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
9 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
10 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
11 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
12 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
13 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
14 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
15 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
16 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
17 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
18 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
19 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
20 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
21 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
22 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
23 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
24 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
25 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
26 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
27 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
28 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
29 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
30 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
31 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
32 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
2 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 33 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
3 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 34 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
4 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 35 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
5 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 36 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
6 -"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
7 -"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
8 -"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
9 -"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
10 -"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
11 -"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
12 -"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
13 -"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
14 -"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
15 -"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
16 -"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
17 -"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
18 -"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
19 -"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
20 -"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
21 -"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
22 -"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
23 -"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
24 -"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
25 -"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
26 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 37 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
27 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 38 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
28 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 39 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -71,25 +82,6 @@ ...@@ -71,25 +82,6 @@
71 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 82 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
72 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 83 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
73 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 84 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
74 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
75 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
76 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
77 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
78 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
79 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
80 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
81 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
82 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
83 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
84 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
85 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
86 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
87 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
88 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
89 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
90 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
91 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
92 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
93 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 85 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
94 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 86 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
95 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 87 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -115,22 +107,42 @@ ...@@ -115,22 +107,42 @@
115 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 107 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
116 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 108 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
117 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 109 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
118 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 110 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
119 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 111 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
120 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 112 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
121 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 113 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
122 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 114 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
123 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 115 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
124 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 116 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
125 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 117 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
126 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 118 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
127 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 119 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
128 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 120 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
129 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 121 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
130 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 122 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
131 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 123 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
132 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 124 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
133 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 125 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
126 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
127 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
128 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
129 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
130 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
131 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
132 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
133 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
134 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
135 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
136 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
137 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
138 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
139 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
140 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
141 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
142 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
143 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
144 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
145 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
134 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 146 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
135 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 147 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
136 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 148 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
...@@ -146,15 +158,3 @@ ...@@ -146,15 +158,3 @@
146 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 158 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
147 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 159 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
148 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask","" 160 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
149 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
150 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
151 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
152 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
153 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
154 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
155 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
156 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
157 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
158 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
159 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
160 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
3 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
4 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
5 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
6 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
7 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
8 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
9 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
10 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
11 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
12 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
13 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
14 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
15 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
16 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
17 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
18 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
19 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
20 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
21 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
22 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
23 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
24 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
25 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
26 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
27 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
28 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
29 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
30 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
31 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
32 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
33 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
34 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
35 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
36 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
37 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
38 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
39 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
40 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
41 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
42 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
43 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
44 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
45 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
46 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
47 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
48 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
49 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
50 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
51 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
52 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
53 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
54 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
2 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 55 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
3 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 56 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
4 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 57 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
5 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 58 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
6 -"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
7 -"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
8 -"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
9 -"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
10 -"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
11 -"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
12 -"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
13 -"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
14 -"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
15 -"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
16 -"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
17 -"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
18 -"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
19 -"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
20 -"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
21 -"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
22 -"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
23 -"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
24 -"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
25 -"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
26 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 59 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
27 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 60 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
28 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 61 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -71,25 +104,6 @@ ...@@ -71,25 +104,6 @@
71 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 104 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
72 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 105 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
73 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 106 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
74 -"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
75 -"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
76 -"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
77 -"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
78 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
79 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
80 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
81 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
82 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
83 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
84 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
85 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
86 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
87 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
88 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
89 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
90 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
91 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
92 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
93 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 107 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
94 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 108 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
95 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 109 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -115,22 +129,42 @@ ...@@ -115,22 +129,42 @@
115 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 129 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
116 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 130 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
117 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 131 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
118 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 132 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
119 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 133 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
120 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 134 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
121 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 135 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
122 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 136 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
123 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 137 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
124 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 138 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
125 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 139 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
126 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 140 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
127 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 141 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
128 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 142 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
129 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 143 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
130 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 144 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
131 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 145 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
132 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 146 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
133 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 147 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
148 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
149 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
150 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
151 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
152 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
153 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
154 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
155 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
156 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
157 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
158 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
159 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
160 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
161 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
162 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
163 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
164 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
165 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
166 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
167 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
134 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 168 "GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
135 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 169 "GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
136 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 170 "GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
...@@ -146,37 +180,3 @@ ...@@ -146,37 +180,3 @@
146 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 180 "GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
147 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask","" 181 "GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
148 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask","" 182 "GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
149 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
150 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
151 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
152 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
153 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
154 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
155 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
156 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
157 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
158 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
159 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
160 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
161 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
162 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
163 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
164 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
165 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
166 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
167 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
168 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
169 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
170 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
171 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
172 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
173 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
174 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
175 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
176 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
177 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
178 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
179 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
180 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
181 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
182 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
......
1 +"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
5 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
6 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
7 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
8 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
9 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
10 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
11 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
12 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
14 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
15 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
16 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
17 +"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
18 +"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
19 +"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
20 +"GSE41195","GSM1010202","","","","","","","","","","","","","","","","","","",""
21 +"GSE41195","GSM1010203","","","","","","","","","","","","","","","","","","",""
22 +"GSE41195","GSM1010204","","","","","","","","","","","","","","","","","","",""
23 +"GSE41195","GSM1010205","","","","","","","","","","","","","","","","","","",""
24 +"GSE41195","GSM1010206","","","","","","","","","","","","","","","","","","",""
25 +"GSE41195","GSM1010207","","","","","","","","","","","","","","","","","","",""
26 +"GSE41195","GSM1010208","","","","","","","","","","","","","","","","","","",""
27 +"GSE41195","GSM1010209","","","","","","","","","","","","","","","","","","",""
28 +"GSE41195","GSM1010210","","","","","","","","","","","","","","","","","","",""
29 +"GSE41195","GSM1010211","","","","","","","","","","","","","","","","","","",""
30 +"GSE41195","GSM1010212","","","","","","","","","","","","","","","","","","",""
31 +"GSE41195","GSM1010213","","","","","","","","","","","","","","","","","","",""
32 +"GSE41195","GSM1010214","","","","","","","","","","","","","","","","","","",""
33 +"GSE41195","GSM1010215","","","","","","","","","","","","","","","","","","",""
34 +"GSE41195","GSM1010216","","","","","","","","","","","","","","","","","","",""
35 +"GSE41195","GSM1010217","","","","","","","","","","","","","","","","","","",""
36 +"GSE41195","GSM1010218","","","","","","","","","","","","","","","","","","",""
37 +"GSE41195","GSM1010219","","","","","","","","","","","","","","","","","","",""
38 +"GSE41195","GSM1010220","","","","","","","","","","","","","","","","","","",""
39 +"GSE41195","GSM1010221","","","","","","","","","","","","","","","","","","",""
40 +"GSE41195","GSM1010222","","","","","","","","","","","","","","","","","","",""
41 +"GSE41195","GSM1010223","","","","","","","","","","","","","","","","","","",""
42 +"GSE41195","GSM1010224","","","","","","","","","","","","","","","","","","",""
43 +"GSE41195","GSM1010240","","","","","","","","","","","","","","","","","","",""
44 +"GSE41195","GSM1010241","","","","","","","","","","","","","","","","","","",""
45 +"GSE41195","GSM1010242","","","","","","","","","","","","","","","","","","",""
46 +"GSE41195","GSM1010243","","","","","","","","","","","","","","","","","","",""
47 +"GSE41195","GSM1010244","","","","","","","","","","","","","","","","","","",""
48 +"GSE41195","GSM1010245","","","","","","","","","","","","","","","","","","",""
49 +"GSE41195","GSM1010246","","","","","","","","","","","","","","","","","","",""
50 +"GSE41195","GSM1010247","","","","","","","","","","","","","","","","","","",""
51 +"GSE41195","GSM1054383","","","","","","","","","","","","","","","","","","",""
52 +"GSE41195","GSM1054384","","","","","","","","","","","","","","","","","","",""
53 +"GSE41195","GSM1072326","","","","","","","","","","","","","","","","","","",""
54 +"GSE41195","GSM1072327","","","","","","","","","","","","","","","","","","",""
55 +"GSE41195","GSM1072328","","","","","","","","","","","","","","","","","","",""
56 +"GSE41195","GSM1124977","","","","","","","","","","","","","","","","","","",""
57 +"GSE41195","GSM1124978","","","","","","","","","","","","","","","","","","",""
58 +"GSE41195","GSM1124979","","","","","","","","","","","","","","","","","","",""
59 +"GSE41195","GSM1124980","","","","","","","","","","","","","","","","","","",""
60 +"GSE41195","GSM1126445","","","","","","","","","","","","","","","","","","",""
61 +"GSE41195","GSM1126446","","","","","","","","","","","","","","","","","","",""
62 +"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
63 +"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
64 +"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
65 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
66 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
67 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
68 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
69 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
70 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
71 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
72 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
73 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
74 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
75 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
76 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
77 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
78 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
79 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
80 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
81 +"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
82 +"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
83 +"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
84 +"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
85 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
86 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
87 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
88 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
89 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
90 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
91 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
92 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
93 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
94 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
95 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
96 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
97 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
98 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
99 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
100 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
101 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
102 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
103 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
104 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
105 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
106 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
107 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
108 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
109 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
110 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
111 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
112 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
113 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
114 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
115 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
116 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
117 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
118 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
119 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
120 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
121 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
122 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
123 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
124 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
125 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
126 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
127 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
128 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
129 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
130 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
131 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
132 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
133 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
134 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
135 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
136 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
137 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
138 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
139 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
140 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
141 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
142 +"GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
143 +"GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
144 +"GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
145 +"GSE41186","GSM1010202","ß - Anaerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
146 +"GSE41186","GSM1010203","ß - Anaerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
147 +"GSE41186","GSM1010204","ß - Aerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
148 +"GSE41186","GSM1010205","ß - Aerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
149 +"GSE41186","GSM1010206","HNS - Anaerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
150 +"GSE41186","GSM1010207","HNS - Aerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
151 +"GSE41186","GSM1010208","IHF - Anaerobic A","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
152 +"GSE41186","GSM1010209","∆fnr - Anaeroibc","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","∆fnr, PK4854","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
153 +"GSE41186","GSM1010210","Ptac::fnr - A - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
154 +"GSE41186","GSM1010211","Ptac::fnr - B - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
155 +"GSE41186","GSM1010212","Ptac::fnr - A - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
156 +"GSE41186","GSM1010213","Ptac::fnr - B - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
157 +"GSE41186","GSM1010214","Ptac::fnr - A - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
158 +"GSE41186","GSM1010215","Ptac::fnr - B - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
159 +"GSE41186","GSM1010216","Ptac::fnr - C - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
160 +"GSE41186","GSM1010217","FNR - Anaerobic - Affinity Purified - A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
161 +"GSE41186","GSM1010218","FNR - Anaerobic - Affinity Purified - B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
162 +"GSE41186","GSM1054383","FNR - ∆hns∆stpA A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
163 +"GSE41186","GSM1054384","FNR - ∆hns∆stpA B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
164 +"GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
165 +"GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
166 +"GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
167 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
168 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
169 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
170 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
171 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
172 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
173 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
174 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
175 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
176 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
177 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
178 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
179 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
180 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
181 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
182 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
183 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
184 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
185 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
186 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
187 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
188 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
189 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
190 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
191 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
192 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
193 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
194 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
195 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
196 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
197 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
198 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
199 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
200 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
2 "GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 "GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 "GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 "GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 "GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 "GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
...@@ -11,44 +14,18 @@ ...@@ -11,44 +14,18 @@
11 "GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 14 "GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 "GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 15 "GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 "GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 16 "GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 17 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
15 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 18 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
16 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 19 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
17 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 20 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
18 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 21 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
19 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 22 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
20 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 23 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
21 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 24 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
22 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 25 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
23 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 26 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
24 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 27 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
25 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 28 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
26 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
27 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
28 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
29 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
30 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
31 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
32 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
33 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
34 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
35 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
36 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
37 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
38 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
39 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
40 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
41 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
42 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
43 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
44 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
45 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
46 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
49 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
50 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
51 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
52 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 29 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
53 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 30 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
54 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 31 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -97,34 +74,41 @@ ...@@ -97,34 +74,41 @@
97 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 74 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
98 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 75 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
99 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 76 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
77 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
78 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
79 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
80 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
81 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
82 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
83 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
84 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
85 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
86 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
87 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
88 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
89 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 93 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
101 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 94 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
102 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 95 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
103 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 96 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
104 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 97 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
105 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 98 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
106 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 99 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
107 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 100 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
108 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 101 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
109 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 102 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
110 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 103 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
111 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 104 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
112 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 105 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
113 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 106 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
114 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 107 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
115 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 108 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
116 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 109 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
117 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 110 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
118 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 111 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
119 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
120 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
121 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
122 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
123 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
124 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
125 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
126 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
127 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
128 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 112 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
129 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 113 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
130 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 114 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -145,6 +129,28 @@ ...@@ -145,6 +129,28 @@
145 "GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","","" 129 "GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
146 "GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 130 "GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
147 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 131 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
132 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
133 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
134 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
135 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
136 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
137 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
138 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
139 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
140 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
141 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
142 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
143 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
144 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
145 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
146 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
147 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
148 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
149 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
150 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
151 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
152 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
153 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
148 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 154 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
149 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 155 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
150 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 156 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -170,25 +176,37 @@ ...@@ -170,25 +176,37 @@
170 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 176 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
171 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 177 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
172 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 178 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
173 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 179 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
174 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 180 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
175 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 181 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
176 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 182 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
177 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 183 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
178 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 184 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
179 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 185 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
180 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 186 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
181 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 187 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
182 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 188 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
183 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 189 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
184 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 190 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
185 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 191 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
186 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 192 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
187 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 193 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
188 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 194 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
189 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 195 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
190 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 196 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
191 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 197 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
192 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 198 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
193 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 199 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
194 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 200 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
201 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
202 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
203 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
204 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
205 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
206 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
207 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
208 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
209 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
210 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
211 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
212 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
2 "GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 "GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 "GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 "GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 "GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 "GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
...@@ -11,44 +14,18 @@ ...@@ -11,44 +14,18 @@
11 "GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 14 "GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 "GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 15 "GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 "GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 16 "GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 17 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
15 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 18 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
16 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 19 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
17 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 20 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
18 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 21 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
19 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 22 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
20 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 23 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
21 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 24 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
22 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 25 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
23 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 26 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
24 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 27 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
25 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 28 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
26 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
27 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
28 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
29 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
30 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
31 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
32 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
33 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
34 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
35 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
36 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
37 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
38 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
39 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
40 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
41 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
42 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
43 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
44 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
45 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
46 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
49 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
50 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
51 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
52 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 29 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
53 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 30 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
54 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 31 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -97,34 +74,41 @@ ...@@ -97,34 +74,41 @@
97 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 74 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
98 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 75 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
99 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 76 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
77 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
78 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
79 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
80 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
81 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
82 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
83 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
84 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
85 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
86 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
87 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
88 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
89 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 93 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
101 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 94 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
102 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 95 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
103 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 96 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
104 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 97 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
105 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 98 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
106 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 99 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
107 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 100 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
108 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 101 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
109 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 102 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
110 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 103 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
111 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 104 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
112 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 105 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
113 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 106 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
114 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 107 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
115 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 108 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
116 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 109 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
117 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 110 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
118 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 111 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
119 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
120 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
121 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
122 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
123 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
124 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
125 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
126 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
127 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
128 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 112 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
129 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 113 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
130 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 114 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -147,6 +131,28 @@ ...@@ -147,6 +131,28 @@
147 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 131 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
148 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 132 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
149 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 133 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
134 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
135 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
136 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
137 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
138 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
139 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
140 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
141 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
142 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
143 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
144 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
145 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
146 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
147 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
148 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
149 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
150 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
151 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
152 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
153 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
154 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
155 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
150 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 156 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
151 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 157 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
152 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 158 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -172,25 +178,37 @@ ...@@ -172,25 +178,37 @@
172 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 178 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
173 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 179 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
174 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 180 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
175 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 181 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
176 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 182 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
177 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 183 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
178 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 184 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
179 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 185 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
180 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 186 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
181 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 187 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
182 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 188 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
183 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 189 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
184 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 190 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
185 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 191 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
186 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 192 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
187 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 193 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
188 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 194 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
189 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 195 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
190 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 196 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
191 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 197 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
192 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 198 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
193 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 199 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
194 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 200 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
195 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 201 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
196 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 202 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
203 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
204 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
205 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
206 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
207 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
208 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
209 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
210 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
211 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
212 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
213 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
214 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
3 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
4 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
2 "GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 "GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 "GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 "GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 "GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 "GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
...@@ -11,56 +14,18 @@ ...@@ -11,56 +14,18 @@
11 "GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 14 "GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 "GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 15 "GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 "GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 16 "GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 17 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
15 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 18 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
16 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","","" 19 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
17 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 20 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
18 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 21 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
19 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 22 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
20 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 23 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
21 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 24 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
22 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 25 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
23 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 26 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
24 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 27 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
25 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","","" 28 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
26 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
27 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
28 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
29 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
30 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
31 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
32 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
33 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
34 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
35 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
36 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
37 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
38 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
39 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
40 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
41 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
42 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
43 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
44 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
45 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
46 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
49 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
50 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
51 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
52 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
53 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
54 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
55 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
56 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
57 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
58 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
59 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
60 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
61 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
62 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
63 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
64 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 29 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
65 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 30 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
66 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 31 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -109,34 +74,53 @@ ...@@ -109,34 +74,53 @@
109 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 74 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
110 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 75 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
111 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 76 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
77 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
78 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
79 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
80 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
81 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
82 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
83 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
84 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
85 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
86 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
87 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
88 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
89 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
94 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
95 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
96 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
97 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
98 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
99 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
100 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
101 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
102 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
103 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
104 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 105 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
113 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 106 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
114 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 107 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
115 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 108 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
116 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 109 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
117 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 110 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
118 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 111 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
119 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 112 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
120 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 113 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
121 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 114 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
122 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 115 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
123 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 116 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
124 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 117 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
125 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 118 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
126 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 119 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
127 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 120 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
128 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 121 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
129 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 122 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
130 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 123 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
131 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
132 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
133 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
134 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
135 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
136 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
137 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
138 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
139 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
140 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 124 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
141 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 125 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
142 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 126 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -159,6 +143,28 @@ ...@@ -159,6 +143,28 @@
159 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 143 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
160 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 144 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
161 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 145 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
146 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
147 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
148 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
149 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
150 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
151 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
152 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
153 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
154 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
155 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
156 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
157 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
158 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
159 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
160 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
161 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
162 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
163 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
164 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
165 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
166 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
167 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
162 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 168 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
163 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 169 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
164 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 170 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -184,25 +190,37 @@ ...@@ -184,25 +190,37 @@
184 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 190 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
185 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 191 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
186 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 192 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
187 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 193 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
188 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 194 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
189 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 195 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
190 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 196 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
191 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 197 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
192 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 198 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
193 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 199 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
194 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 200 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
195 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 201 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
196 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 202 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
197 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 203 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
198 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 204 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
199 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 205 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
200 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 206 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
201 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 207 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
202 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 208 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
203 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 209 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
204 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 210 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
205 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 211 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
206 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 212 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
207 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 213 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
208 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 214 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
215 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
216 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
217 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
218 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
219 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
220 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
221 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
222 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
223 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
224 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
225 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
226 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
15 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
16 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
17 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
18 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
19 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
20 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
21 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
22 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
23 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
24 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
25 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
26 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
27 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
28 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
29 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
30 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
31 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
32 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
33 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
34 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
35 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
36 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
37 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
38 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
39 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
40 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
41 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
42 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
43 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
44 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
45 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
46 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
49 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
50 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -57,22 +11,33 @@ ...@@ -57,22 +11,33 @@
57 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
58 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
59 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
60 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
61 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
62 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
63 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 17 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
64 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 18 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
65 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 19 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
66 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 20 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
67 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 21 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
68 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 22 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
69 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 23 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
70 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 24 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
71 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 25 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
72 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 26 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
73 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 27 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
74 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 28 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
75 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 29 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
30 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
31 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
32 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
33 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
34 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
35 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
36 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
37 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
38 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
39 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
40 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
76 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 41 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
77 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 42 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
78 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 43 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -121,34 +86,53 @@ ...@@ -121,34 +86,53 @@
121 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 86 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
122 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 87 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
123 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 88 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
89 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
94 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
95 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
96 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
97 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
98 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
99 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
101 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
102 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
103 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
104 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
105 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
106 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
107 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
108 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
109 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
110 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
111 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
113 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
114 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
115 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
116 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
124 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 117 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
125 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 118 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
126 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 119 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
127 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 120 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
128 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 121 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
129 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 122 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
130 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 123 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
131 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 124 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
132 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 125 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
133 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 126 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
134 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 127 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
135 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 128 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
136 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 129 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
137 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 130 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
138 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 131 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
139 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 132 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
140 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 133 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
141 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 134 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
142 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 135 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
143 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
144 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
145 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
146 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
147 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
148 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
149 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
150 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
151 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
152 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 136 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
153 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 137 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
154 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 138 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -171,6 +155,28 @@ ...@@ -171,6 +155,28 @@
171 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 155 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
172 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 156 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
173 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 157 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
158 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
159 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
160 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
161 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
162 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
163 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
164 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
165 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
166 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
167 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
168 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
169 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
170 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
171 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
172 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
173 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
174 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
175 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
176 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
177 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
178 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
179 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
174 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 180 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
175 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 181 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
176 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 182 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -196,25 +202,37 @@ ...@@ -196,25 +202,37 @@
196 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 202 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
197 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 203 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
198 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 204 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
199 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 205 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
200 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 206 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
201 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 207 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
202 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 208 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
203 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 209 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
204 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 210 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
205 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 211 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
206 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 212 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
207 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 213 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
208 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 214 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
209 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 215 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
210 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 216 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
211 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 217 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
212 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 218 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
213 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 219 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
214 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 220 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
215 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 221 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
216 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 222 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
217 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 223 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
218 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 224 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
219 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 225 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
220 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 226 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
227 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
228 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
229 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
230 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
231 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
232 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
233 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
234 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
235 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
236 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
237 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
238 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
15 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
16 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
17 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
18 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
19 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
20 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
21 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
22 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
23 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
24 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
25 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
26 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
27 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
28 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
29 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
30 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
31 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
32 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
33 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
34 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
35 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
36 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
37 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
38 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
39 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
40 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
41 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
42 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
43 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
44 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
45 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
46 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
49 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
50 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
51 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
52 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
53 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
54 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
55 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
56 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -63,22 +11,33 @@ ...@@ -63,22 +11,33 @@
63 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
64 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
65 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
66 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
67 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
68 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
69 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 17 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
70 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 18 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
71 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 19 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
72 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 20 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
73 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 21 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
74 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 22 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
75 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 23 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
76 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 24 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
77 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 25 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
78 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 26 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
79 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 27 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
80 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 28 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
81 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 29 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
30 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
31 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
32 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
33 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
34 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
35 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
36 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
37 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
38 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
39 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
40 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
82 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 41 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
83 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 42 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
84 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 43 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -127,34 +86,59 @@ ...@@ -127,34 +86,59 @@
127 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 86 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
128 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 87 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
129 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 88 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
89 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
94 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
95 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
96 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
97 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
98 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
99 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
101 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
102 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
103 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
104 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
105 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
106 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
107 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
108 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
109 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
110 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
111 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
113 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
114 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
115 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
116 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
130 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 117 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
131 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 118 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
132 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 119 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
133 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 120 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
134 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 121 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
135 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 122 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
136 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 123 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
137 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 124 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
138 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 125 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
139 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 126 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
140 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 127 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
141 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 128 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
142 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 129 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
143 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 130 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
144 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 131 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
145 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 132 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
146 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 133 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
147 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 134 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
148 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 135 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
149 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 136 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
150 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 137 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
151 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 138 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
152 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 139 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
153 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 140 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
154 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 141 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
155 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
156 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
157 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
158 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 142 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
159 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 143 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
160 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 144 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -177,6 +161,28 @@ ...@@ -177,6 +161,28 @@
177 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 161 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
178 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 162 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
179 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 163 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
164 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
165 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
166 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
167 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
168 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
169 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
170 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
171 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
172 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
173 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
174 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
175 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
176 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
177 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
178 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
179 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
180 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
181 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
182 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
183 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
184 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
185 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
180 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 186 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
181 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 187 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
182 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 188 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -202,25 +208,37 @@ ...@@ -202,25 +208,37 @@
202 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 208 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
203 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 209 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
204 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 210 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
205 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 211 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
206 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 212 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
207 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 213 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
208 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 214 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
209 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 215 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
210 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 216 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
211 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 217 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
212 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 218 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
213 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 219 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
214 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 220 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
215 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 221 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
216 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 222 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
217 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 223 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
218 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 224 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
219 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 225 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
220 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 226 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
221 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 227 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
222 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 228 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
223 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 229 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
224 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 230 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
225 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 231 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
226 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 232 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
233 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
234 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
235 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
236 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
237 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
238 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
239 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
240 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
241 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
242 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
243 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
244 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
15 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
16 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
17 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
18 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
19 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
20 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
21 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
22 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
23 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
24 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
25 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
26 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
27 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
28 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
29 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
30 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
31 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
32 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
33 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
34 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
35 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
36 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
37 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
38 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
39 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
40 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
41 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
42 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
43 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
44 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
45 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
46 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
49 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
50 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
51 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
52 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
53 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
54 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
55 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
56 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
57 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
58 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
59 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
60 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
61 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
62 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
63 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
64 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -71,22 +11,33 @@ ...@@ -71,22 +11,33 @@
71 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
72 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
73 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
74 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
75 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
76 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
77 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 17 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
78 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 18 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
79 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 19 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
80 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 20 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
81 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 21 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 22 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
83 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 23 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
84 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 24 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
85 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 25 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 26 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 27 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 28 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 29 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
30 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
31 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
32 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
33 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
34 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
35 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
36 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
37 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
38 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
39 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
40 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
90 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 41 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
91 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 42 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
92 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 43 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -135,34 +86,59 @@ ...@@ -135,34 +86,59 @@
135 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 86 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
136 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 87 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
137 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 88 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
89 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
94 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
95 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
96 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
97 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
98 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
99 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
101 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
102 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
103 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
104 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
105 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
106 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
107 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
108 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
109 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
110 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
111 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
113 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
114 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
115 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
116 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
138 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 117 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
139 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 118 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
140 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 119 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
141 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 120 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
142 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 121 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
143 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 122 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
144 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 123 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
145 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 124 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
146 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 125 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
147 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 126 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
148 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 127 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
149 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 128 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
150 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 129 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
151 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 130 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
152 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 131 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
153 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 132 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
154 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 133 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
155 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 134 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
156 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 135 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
157 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 136 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
158 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 137 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
159 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 138 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
160 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 139 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
161 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 140 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
162 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 141 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
163 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
164 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
165 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
166 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 142 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
167 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 143 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
168 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 144 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -185,6 +161,28 @@ ...@@ -185,6 +161,28 @@
185 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 161 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
186 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 162 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
187 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 163 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
164 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
165 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
166 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
167 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
168 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
169 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
170 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
171 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
172 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
173 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
174 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
175 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
176 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
177 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
178 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
179 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
180 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
181 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
182 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
183 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
184 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
185 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
188 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 186 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
189 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 187 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
190 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 188 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -210,25 +208,45 @@ ...@@ -210,25 +208,45 @@
210 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 208 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
211 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 209 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
212 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 210 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
213 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 211 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
214 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 212 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
215 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 213 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
216 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 214 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
217 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 215 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
218 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 216 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
219 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 217 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
220 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 218 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
221 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 219 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
222 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 220 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
223 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 221 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
224 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 222 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
225 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 223 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
226 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 224 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
227 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 225 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
228 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 226 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
229 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 227 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
230 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 228 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
231 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 229 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
232 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 230 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
233 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 231 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
234 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 232 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
233 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
234 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
235 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
236 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
237 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
238 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
239 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
240 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
241 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
242 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
243 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
244 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
245 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
246 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
247 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
248 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
249 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
250 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
251 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
252 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
15 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
16 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
17 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
18 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
19 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
20 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
21 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
22 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
23 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
24 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
25 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
26 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
27 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
28 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
29 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
30 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
31 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
32 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
33 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
34 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
35 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
36 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
37 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
38 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
39 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
40 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
41 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
42 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
43 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
44 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
45 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
46 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
49 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
50 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
51 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
52 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
53 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
54 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
55 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
56 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
57 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
58 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
59 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
60 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
61 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
62 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
63 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
64 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -71,22 +11,33 @@ ...@@ -71,22 +11,33 @@
71 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
72 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
73 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
74 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
75 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
76 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
77 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 17 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
78 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 18 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
79 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 19 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
80 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 20 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
81 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 21 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 22 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
83 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 23 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
84 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 24 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
85 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 25 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 26 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 27 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 28 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 29 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
30 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
31 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
32 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
33 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
34 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
35 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
36 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
37 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
38 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
39 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
40 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
90 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 41 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
91 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 42 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
92 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 43 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -135,34 +86,59 @@ ...@@ -135,34 +86,59 @@
135 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 86 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
136 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 87 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
137 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 88 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
89 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
94 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
95 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
96 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
97 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
98 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
99 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
101 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
102 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
103 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
104 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
105 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
106 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
107 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
108 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
109 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
110 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
111 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
113 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
114 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
115 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
116 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
138 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 117 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
139 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 118 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
140 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 119 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
141 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 120 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
142 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 121 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
143 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 122 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
144 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 123 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
145 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 124 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
146 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 125 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
147 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 126 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
148 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 127 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
149 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 128 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
150 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 129 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
151 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 130 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
152 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 131 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
153 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 132 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
154 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 133 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
155 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 134 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
156 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 135 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
157 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 136 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
158 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 137 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
159 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 138 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
160 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 139 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
161 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 140 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
162 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 141 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
163 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
164 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
165 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
166 "GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 142 "GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
167 "GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 143 "GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
168 "GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 144 "GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
...@@ -193,6 +169,28 @@ ...@@ -193,6 +169,28 @@
193 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 169 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
194 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 170 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
195 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 171 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
172 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
173 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
174 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
175 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
176 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
177 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
178 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
179 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
180 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
181 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
182 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
183 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
184 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
185 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
186 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
187 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
188 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
189 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
190 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
191 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
192 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
193 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
196 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 194 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
197 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 195 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
198 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 196 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -218,25 +216,45 @@ ...@@ -218,25 +216,45 @@
218 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 216 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
219 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 217 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
220 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 218 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
221 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 219 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
222 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 220 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
223 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 221 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
224 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 222 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
225 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 223 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
226 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 224 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
227 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 225 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
228 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 226 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
229 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 227 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
230 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 228 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
231 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 229 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
232 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 230 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
233 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 231 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
234 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 232 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
235 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 233 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
236 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 234 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
237 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 235 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
238 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 236 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
239 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 237 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
240 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 238 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
241 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 239 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
242 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 240 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
241 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
242 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
243 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
244 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
245 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
246 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
247 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
248 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
249 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
250 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
251 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
252 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
253 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
254 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
255 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
256 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
257 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
258 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
259 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
260 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
14 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
15 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
16 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
17 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
18 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
19 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
20 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
21 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
22 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
23 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
24 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
25 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
26 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
27 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
28 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
29 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
30 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
31 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
32 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
33 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
34 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
35 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
36 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
37 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
38 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
39 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
40 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
41 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
42 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
43 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
44 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
45 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
46 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
47 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
48 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
49 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
50 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
51 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
52 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
53 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
54 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
55 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
56 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
57 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
58 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
59 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
60 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
61 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
62 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
63 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
64 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
65 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
66 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
67 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
68 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
69 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
70 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
71 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
72 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -79,22 +11,33 @@ ...@@ -79,22 +11,33 @@
79 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
80 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
81 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
83 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
84 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
85 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 17 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 18 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 19 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 20 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 21 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
90 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 22 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
91 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 23 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
92 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 24 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
93 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 25 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
94 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 26 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
95 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 27 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
96 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 28 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
97 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 29 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
30 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
31 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
32 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
33 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
34 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
35 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
36 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
37 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
38 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
39 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
40 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
98 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 41 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
99 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 42 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
100 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 43 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -143,34 +86,59 @@ ...@@ -143,34 +86,59 @@
143 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 86 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
144 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 87 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
145 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 88 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
89 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
94 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
95 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
96 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
97 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
98 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
99 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
101 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
102 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
103 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
104 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
105 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
106 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
107 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
108 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
109 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
110 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
111 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
113 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
114 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
115 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
116 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
146 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 117 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
147 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 118 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
148 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 119 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
149 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 120 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
150 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 121 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
151 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 122 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
152 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 123 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
153 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 124 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
154 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 125 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
155 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 126 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
156 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 127 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
157 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 128 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
158 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 129 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
159 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 130 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
160 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 131 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
161 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 132 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
162 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 133 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
163 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 134 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
164 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 135 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
165 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 136 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
166 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 137 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
167 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 138 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
168 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 139 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
169 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 140 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
170 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 141 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
171 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
172 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
173 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
174 "GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 142 "GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
175 "GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 143 "GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
176 "GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 144 "GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
...@@ -201,6 +169,28 @@ ...@@ -201,6 +169,28 @@
201 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 169 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
202 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 170 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
203 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 171 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
172 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
173 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
174 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
175 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
176 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
177 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
178 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
179 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
180 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
181 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
182 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
183 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
184 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
185 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
186 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
187 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
188 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
189 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
190 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
191 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
192 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
193 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
204 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 194 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
205 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 195 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
206 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 196 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -226,25 +216,53 @@ ...@@ -226,25 +216,53 @@
226 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 216 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
227 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 217 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
228 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 218 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
229 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 219 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
230 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 220 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
231 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 221 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
232 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 222 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
233 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 223 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
234 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 224 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
235 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 225 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
236 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 226 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
237 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 227 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
238 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 228 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
239 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 229 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
240 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 230 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
241 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 231 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
242 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 232 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
243 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 233 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
244 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 234 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
245 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 235 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
246 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 236 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
247 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 237 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
248 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 238 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
249 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 239 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
250 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 240 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
241 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
242 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
243 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
244 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
245 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
246 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
247 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
248 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
249 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
250 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
251 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
252 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
253 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
254 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
255 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
256 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
257 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
258 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
259 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
260 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
261 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
262 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
263 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
264 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
265 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
266 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
267 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
268 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
3 -"GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
4 -"GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
5 -"GSE74930","GSM1937952","Wild-type Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
6 -"GSE74930","GSM1937953","∆fur Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
7 -"GSE74930","GSM1937954","∆fur Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
8 -"GSE74930","GSM1937955","∆fur Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
9 -"GSE74930","GSM1937956","∆fur Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
10 -"GSE74930","GSM1937957","∆fur ∆ryhB Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
11 -"GSE74930","GSM1937958","∆fur ∆ryhB Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
12 -"GSE74930","GSM1937959","∆fur ∆ryhB Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
13 -"GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
14 -"GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
15 -"GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
16 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
17 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
18 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
19 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
20 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
21 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
22 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
23 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
24 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
25 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
26 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
27 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
28 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
29 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
30 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
31 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
32 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
33 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
34 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
35 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
36 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
37 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
38 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
39 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
40 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
41 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
42 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
43 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
44 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
45 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
46 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
47 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
48 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
49 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
50 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
51 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
52 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
53 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
54 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
55 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
56 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
57 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
58 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
59 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
60 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
61 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
62 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
63 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
64 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
65 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
66 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
67 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
68 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
69 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
70 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
71 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
72 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
73 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
74 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
75 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
76 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
77 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
78 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
79 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
80 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
81 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
82 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
83 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
84 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
85 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
86 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -93,22 +11,33 @@ ...@@ -93,22 +11,33 @@
93 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
94 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
95 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
96 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
97 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
98 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
99 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 17 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
100 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 18 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
101 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 19 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
102 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 20 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
103 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 21 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
104 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 22 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
105 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 23 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
106 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 24 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
107 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 25 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
108 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 26 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
109 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 27 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
110 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 28 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
111 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 29 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
30 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
31 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
32 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
33 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
34 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
35 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
36 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
37 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
38 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
39 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
40 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
112 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 41 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
113 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 42 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
114 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 43 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -157,34 +86,73 @@ ...@@ -157,34 +86,73 @@
157 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 86 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
158 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 87 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
159 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 88 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
89 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
90 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
91 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
92 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
93 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
94 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
95 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
96 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
97 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
98 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
99 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
100 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
101 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
102 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
103 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
104 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
105 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
106 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
107 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
108 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
109 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
110 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
111 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
112 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
113 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
114 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
115 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
116 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
160 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 117 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
161 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 118 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
162 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 119 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
163 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 120 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
164 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 121 +"GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
165 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 122 +"GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
166 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 123 +"GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
167 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 124 +"GSE74930","GSM1937952","Wild-type Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
168 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 125 +"GSE74930","GSM1937953","∆fur Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
169 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 126 +"GSE74930","GSM1937954","∆fur Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
170 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 127 +"GSE74930","GSM1937955","∆fur Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
171 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 128 +"GSE74930","GSM1937956","∆fur Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
172 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 129 +"GSE74930","GSM1937957","∆fur ∆ryhB Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
173 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 130 +"GSE74930","GSM1937958","∆fur ∆ryhB Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
174 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 131 +"GSE74930","GSM1937959","∆fur ∆ryhB Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
175 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 132 +"GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
176 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 133 +"GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
177 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 134 +"GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
178 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 135 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
179 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 136 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
180 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 137 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
181 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 138 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
182 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 139 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
183 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 140 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
184 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 141 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
185 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","","" 142 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
186 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","","" 143 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
187 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","","" 144 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
145 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
146 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
147 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
148 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
149 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
150 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
151 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
152 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
153 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
154 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
155 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
188 "GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 156 "GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
189 "GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 157 "GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
190 "GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 158 "GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
...@@ -215,6 +183,28 @@ ...@@ -215,6 +183,28 @@
215 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 183 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
216 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 184 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
217 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 185 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
186 +"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
187 +"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
188 +"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
189 +"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
190 +"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
191 +"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
192 +"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
193 +"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
194 +"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
195 +"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
196 +"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
197 +"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
198 +"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
199 +"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
200 +"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
201 +"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","",""
202 +"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
203 +"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
204 +"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
205 +"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
206 +"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
207 +"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
218 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 208 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
219 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 209 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
220 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 210 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -240,25 +230,53 @@ ...@@ -240,25 +230,53 @@
240 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 230 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
241 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 231 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
242 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 232 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
243 -"GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 233 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
244 -"GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 234 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
245 -"GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 235 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
246 -"GSE55199","GSM1331412","LB 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 236 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
247 -"GSE55199","GSM1331413","LB 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 237 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
248 -"GSE55199","GSM1331414","LB 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 238 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
249 -"GSE55199","GSM1331415","LB 2.0 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 239 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
250 -"GSE55199","GSM1331416","LB 2.0 B1 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 240 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
251 -"GSE55199","GSM1331417","LB 2.0 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 241 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
252 -"GSE55199","GSM1331418","LB 2.0 B1 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 242 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
253 -"GSE55199","GSM1331419","LB 2.0 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 243 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
254 -"GSE55199","GSM1331420","LB 2.0 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 244 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
255 -"GSE55199","GSM1331421","LB 2.0 B2 TEX neg L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 245 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
256 -"GSE55199","GSM1331422","LB 2.0 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 246 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
257 -"GSE55199","GSM1331423","LB 2.0 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 247 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
258 -"GSE55199","GSM1331424","LB 2.0 B2 TEX pos L2 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of 2.0","stationary","","","" 248 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
259 -"GSE55199","GSM1331425","M63 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 249 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
260 -"GSE55199","GSM1331426","M63 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 250 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
261 -"GSE55199","GSM1331427","M63 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 251 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
262 -"GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 252 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
263 -"GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 253 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
264 -"GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 254 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
255 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
256 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
257 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
258 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
259 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
260 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
261 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
262 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
263 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
264 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
265 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
266 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
267 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
268 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
269 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
270 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
271 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
272 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
273 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
274 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
275 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
276 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
277 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
278 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
279 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
280 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
281 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
282 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
3 -"GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
4 -"GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
5 -"GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
6 -"GSE74930","GSM1937952","Wild-type Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
7 -"GSE74930","GSM1937953","∆fur Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
8 -"GSE74930","GSM1937954","∆fur Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
9 -"GSE74930","GSM1937955","∆fur Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
10 -"GSE74930","GSM1937956","∆fur Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
11 -"GSE74930","GSM1937957","∆fur ∆ryhB Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
12 -"GSE74930","GSM1937958","∆fur ∆ryhB Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
13 -"GSE74930","GSM1937959","∆fur ∆ryhB Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
14 -"GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
15 -"GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
16 -"GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
17 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
18 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
19 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
20 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
21 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
22 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
23 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
24 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
25 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
26 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
27 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
28 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
29 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
30 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
31 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
32 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
33 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
34 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
35 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
36 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
37 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
38 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
39 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
40 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
41 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
42 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
43 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
44 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
45 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
46 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
47 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
48 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
49 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
50 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
51 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
52 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
53 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
54 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
55 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
56 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
57 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
58 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
59 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
60 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
61 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
62 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
63 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
64 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
65 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
66 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
67 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
68 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
69 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
70 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
71 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
72 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
73 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
74 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
75 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
76 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
77 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
78 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
79 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
80 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
81 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
82 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
83 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
84 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
85 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 2 "GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
86 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 3 "GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
87 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 4 "GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
...@@ -94,22 +11,81 @@ ...@@ -94,22 +11,81 @@
94 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 11 "GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
95 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 12 "GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
96 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 13 "GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
17 +"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
18 +"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
19 +"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
20 +"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
21 +"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
22 +"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
23 +"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
24 +"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
25 +"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
26 +"GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
27 +"GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
28 +"GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
29 +"GSE41186","GSM1010202","ß - Anaerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
30 +"GSE41186","GSM1010203","ß - Anaerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
31 +"GSE41186","GSM1010204","ß - Aerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
32 +"GSE41186","GSM1010205","ß - Aerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
33 +"GSE41186","GSM1010206","HNS - Anaerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
34 +"GSE41186","GSM1010207","HNS - Aerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
35 +"GSE41186","GSM1010208","IHF - Anaerobic A","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
36 +"GSE41186","GSM1010209","∆fnr - Anaeroibc","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","∆fnr, PK4854","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
37 +"GSE41186","GSM1010210","Ptac::fnr - A - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
38 +"GSE41186","GSM1010211","Ptac::fnr - B - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
39 +"GSE41186","GSM1010212","Ptac::fnr - A - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
40 +"GSE41186","GSM1010213","Ptac::fnr - B - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
41 +"GSE41186","GSM1010214","Ptac::fnr - A - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
42 +"GSE41186","GSM1010215","Ptac::fnr - B - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
43 +"GSE41186","GSM1010216","Ptac::fnr - C - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
44 +"GSE41186","GSM1010217","FNR - Anaerobic - Affinity Purified - A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
45 +"GSE41186","GSM1010218","FNR - Anaerobic - Affinity Purified - B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
46 +"GSE41186","GSM1054383","FNR - ∆hns∆stpA A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
47 +"GSE41186","GSM1054384","FNR - ∆hns∆stpA B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
48 +"GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
49 +"GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
50 +"GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
51 +"GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
52 +"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
53 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
54 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
55 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
56 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
57 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
58 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
59 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
60 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
61 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
62 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
64 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
65 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
66 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
67 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
68 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
69 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
70 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
71 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
72 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
97 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 73 "GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
98 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 74 "GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
99 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 75 "GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
100 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 76 "GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
101 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 77 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
102 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","","" 78 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
103 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 79 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
104 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","","" 80 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
105 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 81 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
106 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","","" 82 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
107 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 83 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
108 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 84 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
109 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 85 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
110 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 86 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
111 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 87 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
112 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","","" 88 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
113 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 89 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
114 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 90 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
115 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 91 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -158,42 +134,67 @@ ...@@ -158,42 +134,67 @@
158 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 134 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
159 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 135 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
160 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 136 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
137 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
138 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
139 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
140 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
141 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
142 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
143 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
144 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
145 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
146 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
147 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
148 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
149 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
150 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
151 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
152 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
153 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
154 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
155 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
156 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
157 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
158 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
159 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
160 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
161 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
162 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
163 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
164 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
161 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 165 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
162 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 166 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
163 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 167 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
164 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 168 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
165 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 169 +"GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
166 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","","" 170 +"GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
167 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 171 +"GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
168 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","","" 172 +"GSE74930","GSM1937952","Wild-type Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
169 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 173 +"GSE74930","GSM1937953","∆fur Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
170 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 174 +"GSE74930","GSM1937954","∆fur Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
171 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 175 +"GSE74930","GSM1937955","∆fur Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
172 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 176 +"GSE74930","GSM1937956","∆fur Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
173 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 177 +"GSE74930","GSM1937957","∆fur ∆ryhB Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
174 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","","" 178 +"GSE74930","GSM1937958","∆fur ∆ryhB Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
175 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 179 +"GSE74930","GSM1937959","∆fur ∆ryhB Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
176 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","","" 180 +"GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
177 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 181 +"GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
178 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 182 +"GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
179 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 183 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
180 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 184 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
181 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 185 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
182 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 186 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
183 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 187 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
184 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 188 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
185 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 189 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
186 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","","" 190 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
187 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","","" 191 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
188 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","","" 192 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
189 -"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 193 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
190 -"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 194 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
191 -"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 195 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
192 -"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 196 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
193 -"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 197 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
194 -"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
195 -"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
196 -"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
197 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 198 "GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
198 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 199 "GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
199 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 200 "GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
...@@ -214,33 +215,6 @@ ...@@ -214,33 +215,6 @@
214 "GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","","" 215 "GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
215 "GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 216 "GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
216 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 217 "GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
217 -"GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
218 -"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
219 -"GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
220 -"GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
221 -"GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
222 -"GSE41186","GSM1010202","ß - Anaerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
223 -"GSE41186","GSM1010203","ß - Anaerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
224 -"GSE41186","GSM1010204","ß - Aerobic - A","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
225 -"GSE41186","GSM1010205","ß - Aerobic - B","RNA Polymerase ß monoclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
226 -"GSE41186","GSM1010206","HNS - Anaerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
227 -"GSE41186","GSM1010207","HNS - Aerobic A","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Aerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
228 -"GSE41186","GSM1010208","IHF - Anaerobic A","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
229 -"GSE41186","GSM1010209","∆fnr - Anaeroibc","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","∆fnr, PK4854","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
230 -"GSE41186","GSM1010210","Ptac::fnr - A - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
231 -"GSE41186","GSM1010211","Ptac::fnr - B - 4 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","4 µM IPTG, 4 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
232 -"GSE41186","GSM1010212","Ptac::fnr - A - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
233 -"GSE41186","GSM1010213","Ptac::fnr - B - 8 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","8 µM IPTG, 8 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
234 -"GSE41186","GSM1010214","Ptac::fnr - A - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
235 -"GSE41186","GSM1010215","Ptac::fnr - B - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
236 -"GSE41186","GSM1010216","Ptac::fnr - C - 16 µM IPTG","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","PK8263","","","","16 µM IPTG, 16 µM IPTG and 300 µL Cm20","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
237 -"GSE41186","GSM1010217","FNR - Anaerobic - Affinity Purified - A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
238 -"GSE41186","GSM1010218","FNR - Anaerobic - Affinity Purified - B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
239 -"GSE41186","GSM1054383","FNR - ∆hns∆stpA A","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
240 -"GSE41186","GSM1054384","FNR - ∆hns∆stpA B","Affinity Purified FNR antibody","Escherichia coli","K-12","MG1655","∆hns/∆stpA","","","","","anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
241 -"GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
242 -"GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
243 -"GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
244 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 218 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
245 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 219 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
246 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 220 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
...@@ -263,3 +237,47 @@ ...@@ -263,3 +237,47 @@
263 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 237 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
264 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 238 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
265 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 239 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
240 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
241 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
242 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
243 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
244 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
245 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
246 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
247 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
248 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
249 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
250 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
251 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
252 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
253 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
254 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
255 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
256 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
257 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
258 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
259 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
260 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
261 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
262 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
263 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
264 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
265 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
266 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
267 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
268 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
269 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
270 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
271 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
272 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
273 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
274 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
275 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
276 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
277 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
278 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
279 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
280 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
281 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
282 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
283 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 2 +"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 3 +"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 4 +"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 +"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 +"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 +"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 8 +"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 9 +"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 10 +"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 11 +"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 12 +"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 13 +"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
17 +"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
18 +"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
19 +"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
20 +"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
21 +"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
22 +"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
23 +"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
24 +"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
25 +"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
14 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 26 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
15 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 27 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
16 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 28 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -36,112 +48,44 @@ ...@@ -36,112 +48,44 @@
36 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 48 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
37 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 49 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
38 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 50 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
39 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
40 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
41 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
42 -"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
43 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
44 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
45 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
46 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
47 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
48 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
49 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
50 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
51 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
52 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
53 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
54 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
55 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 51 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
56 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 52 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
57 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 53 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
58 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 54 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 55 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
60 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 56 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 57 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
62 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 58 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 59 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 60 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 61 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","","" 62 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","","" 63 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
68 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","","" 64 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","","" 65 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
70 -"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","","" 66 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
71 -"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","","" 67 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
72 -"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","","" 68 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
73 -"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","","" 69 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
74 -"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","","" 70 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
75 -"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","","" 71 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
76 -"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","","" 72 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
77 -"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","","" 73 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
78 -"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","","" 74 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
79 -"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","","" 75 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
80 -"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","","" 76 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
81 -"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","","" 77 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","","" 78 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
83 -"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 79 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
84 -"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 80 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
85 -"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","","" 81 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","","" 82 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 83 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","","" 84 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 85 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
90 -"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 86 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
91 -"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 87 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
92 -"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 88 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
93 -"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
94 -"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
95 -"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
96 -"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
97 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
98 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
99 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
100 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
101 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
102 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
103 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
104 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
105 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
106 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
107 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
108 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
109 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
110 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
111 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
112 -"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
113 -"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
114 -"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
115 -"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
116 -"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
117 -"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
118 -"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
119 -"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
120 -"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
121 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
122 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
123 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
124 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
125 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
126 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
127 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
128 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
129 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
130 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
131 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
132 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
133 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
134 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
135 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
136 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
137 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
138 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
139 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
140 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
141 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
142 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
143 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
144 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
145 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 89 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
146 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 90 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
147 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 91 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -190,46 +134,38 @@ ...@@ -190,46 +134,38 @@
190 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 134 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
191 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 135 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
192 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 136 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
193 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 137 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
194 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 138 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
195 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 139 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
196 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 140 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
197 -"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 141 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
198 -"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 142 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
199 -"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 143 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
200 -"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 144 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
201 -"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 145 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
202 -"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 146 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
203 -"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 147 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
204 -"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 148 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
205 -"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 149 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
206 -"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 150 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
207 -"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 151 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
208 -"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 152 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
153 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
154 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
155 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
156 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
157 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
158 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
159 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
160 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
161 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
162 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
163 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
164 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
209 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 165 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
210 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 166 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
211 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 167 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
212 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 168 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
213 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
214 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
215 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
216 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
217 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
218 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
219 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
220 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
221 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
222 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
223 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
224 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
225 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
226 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
227 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
228 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
229 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
230 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
231 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
232 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
233 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 169 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
234 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 170 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
235 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 171 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
...@@ -244,12 +180,41 @@ ...@@ -244,12 +180,41 @@
244 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 180 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
245 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 181 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
246 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 182 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
247 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 183 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
248 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 184 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
249 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 185 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
250 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 186 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
251 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 187 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
252 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 188 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
189 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
190 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
191 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
192 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
193 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
194 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
195 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
196 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
197 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
198 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
199 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
200 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
201 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
202 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
203 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
204 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
205 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
206 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
207 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
208 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
209 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
210 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
211 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
212 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
213 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
214 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
215 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
216 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
217 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
253 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 218 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
254 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 219 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
255 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 220 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
...@@ -272,3 +237,56 @@ ...@@ -272,3 +237,56 @@
272 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 237 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
273 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 238 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
274 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 239 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
240 +"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
241 +"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
242 +"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
243 +"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
244 +"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
245 +"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
246 +"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
247 +"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
248 +"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
249 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
250 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
251 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
252 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
253 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
254 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
255 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
256 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
257 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
258 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
259 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
260 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
261 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
262 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
263 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
264 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
265 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
266 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
267 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
268 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
269 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
270 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
271 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
272 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
273 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
274 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
275 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
276 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
277 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
278 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
279 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
280 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
281 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
282 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
283 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
284 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
285 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
286 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
287 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
288 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
289 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
290 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
291 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
292 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 2 +"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 3 +"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 4 +"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 +"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 +"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 +"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 8 +"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 9 +"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 10 +"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 11 +"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 12 +"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 13 +"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
17 +"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
18 +"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
19 +"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
20 +"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
21 +"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
22 +"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
23 +"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
24 +"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
25 +"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
14 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 26 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
15 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 27 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
16 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 28 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -36,114 +48,46 @@ ...@@ -36,114 +48,46 @@
36 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 48 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
37 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 49 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
38 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 50 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
39 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
40 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
41 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
42 -"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
43 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
44 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
45 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
46 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
47 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
48 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
49 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
50 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
51 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
52 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
53 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
54 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
55 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 51 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
56 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 52 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
57 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 53 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
58 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 54 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 55 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
60 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 56 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 57 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
62 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 58 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 59 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 60 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 61 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","","" 62 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","","" 63 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
68 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","","" 64 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
70 -"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
71 -"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
72 -"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
73 -"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
74 -"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
75 -"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
76 -"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
77 -"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
78 -"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
79 -"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
80 -"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
81 -"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
83 -"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
84 -"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
85 -"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
90 -"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
91 -"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
92 -"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
93 -"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
94 -"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
95 -"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
96 -"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
97 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
98 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
99 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
100 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
101 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
102 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
103 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
104 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
105 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
106 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
107 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
108 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
109 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
110 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
111 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
112 -"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
113 -"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
114 -"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
115 -"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
116 -"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
117 -"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
118 -"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
119 -"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
120 -"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
121 "GSE88979","GSM2356685","OmpR NaCl 1","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","","" 65 "GSE88979","GSM2356685","OmpR NaCl 1","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","",""
122 "GSE88979","GSM2356686","OmpR NaCl 2","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","","" 66 "GSE88979","GSM2356686","OmpR NaCl 2","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","",""
123 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 67 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
124 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 68 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
125 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 69 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
126 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 70 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
127 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 71 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
128 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 72 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
129 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 73 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
130 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 74 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
131 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 75 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
132 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 76 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
133 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 77 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
134 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 78 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
135 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 79 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
136 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 80 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
137 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 81 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
138 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 82 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
139 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 83 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
140 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 84 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
141 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 85 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
142 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 86 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
143 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 87 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
144 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 88 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
145 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 89 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
146 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 90 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
147 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 91 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
148 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 92 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
149 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 93 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -192,46 +136,38 @@ ...@@ -192,46 +136,38 @@
192 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 136 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
193 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 137 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
194 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 138 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
195 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 139 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
196 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 140 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
197 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 141 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
198 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 142 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
199 -"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 143 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
200 -"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 144 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
201 -"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 145 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
202 -"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 146 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
203 -"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 147 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
204 -"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 148 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
205 -"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 149 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
206 -"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 150 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
207 -"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 151 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
208 -"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 152 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
209 -"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 153 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
210 -"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 154 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
155 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
156 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
157 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
158 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
159 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
160 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
161 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
162 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
163 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
164 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
165 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
166 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
211 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 167 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
212 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 168 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
213 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 169 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
214 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 170 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
215 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
216 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
217 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
218 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
219 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
220 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
221 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
222 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
223 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
224 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
225 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
226 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
227 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
228 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
229 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
230 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
231 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
232 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
233 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
234 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
235 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 171 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
236 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 172 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
237 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 173 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
...@@ -246,12 +182,41 @@ ...@@ -246,12 +182,41 @@
246 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 182 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
247 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 183 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
248 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 184 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
249 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 185 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
250 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 186 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
251 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 187 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
252 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 188 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
253 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 189 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
254 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 190 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
191 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
192 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
193 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
194 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
195 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
196 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
197 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
198 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
199 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
200 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
201 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
202 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
203 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
204 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
205 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
206 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
207 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
208 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
209 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
210 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
211 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
212 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
213 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
214 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
215 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
216 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
217 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
218 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
219 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
255 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 220 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
256 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 221 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
257 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 222 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
...@@ -274,3 +239,56 @@ ...@@ -274,3 +239,56 @@
274 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 239 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
275 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 240 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
276 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 241 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
242 +"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
243 +"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
244 +"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
245 +"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
246 +"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
247 +"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
248 +"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
249 +"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
250 +"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
251 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
252 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
253 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
254 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
255 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
256 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
257 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
258 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
259 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
260 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
261 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
262 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
263 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
264 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
265 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
266 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
267 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
268 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
269 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
270 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
271 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
272 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
273 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
274 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
275 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
276 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
277 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
278 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
279 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
280 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
281 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
282 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
283 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
284 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
285 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
286 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
287 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
288 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
289 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
290 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
291 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
292 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
293 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
294 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 2 +"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 3 +"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 4 +"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 +"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 +"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 +"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 8 +"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 9 +"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 10 +"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 11 +"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 12 +"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 13 +"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
17 +"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
18 +"GSE88980","GSM2356687","WT NaCl 1","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
19 +"GSE88980","GSM2356688","WT NaCl 2","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
20 +"GSE88980","GSM2356689","ΔompR NaCl 1","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
21 +"GSE88980","GSM2356690","ΔompR NaCl 2","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
22 +"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
23 +"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
24 +"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
25 +"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
26 +"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
27 +"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
28 +"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
29 +"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
14 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 30 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
15 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 31 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
16 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 32 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -36,114 +52,46 @@ ...@@ -36,114 +52,46 @@
36 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 52 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
37 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 53 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
38 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 54 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
39 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
40 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
41 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
42 -"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
43 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
44 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
45 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
46 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
47 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
48 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
49 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
50 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
51 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
52 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
53 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
54 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
55 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 55 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
56 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 56 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
57 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 57 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
58 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 58 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 59 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
60 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 60 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 61 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
62 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 62 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 63 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 64 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 65 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","","" 66 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","","" 67 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
68 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","","" 68 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
70 -"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
71 -"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
72 -"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
73 -"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
74 -"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
75 -"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
76 -"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
77 -"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
78 -"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
79 -"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
80 -"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
81 -"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
83 -"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
84 -"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
85 -"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
90 -"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
91 -"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
92 -"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
93 -"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
94 -"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
95 -"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
96 -"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
97 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
98 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
99 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
100 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
101 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
102 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
103 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
104 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
105 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
106 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
107 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
108 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
109 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
110 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
111 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
112 -"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
113 -"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
114 -"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
115 -"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
116 -"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
117 -"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
118 -"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
119 -"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
120 -"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
121 "GSE88979","GSM2356685","OmpR NaCl 1","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","","" 69 "GSE88979","GSM2356685","OmpR NaCl 1","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","",""
122 "GSE88979","GSM2356686","OmpR NaCl 2","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","","" 70 "GSE88979","GSM2356686","OmpR NaCl 2","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","",""
123 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 71 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
124 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 72 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
125 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 73 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
126 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 74 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
127 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 75 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
128 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 76 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
129 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 77 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
130 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 78 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
131 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 79 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
132 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 80 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
133 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 81 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
134 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 82 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
135 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 83 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
136 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 84 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
137 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 85 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
138 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 86 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
139 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 87 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
140 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 88 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
141 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 89 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
142 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 90 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
143 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 91 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
144 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 92 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
145 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 93 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
146 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 94 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
147 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 95 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
148 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 96 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
149 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 97 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -192,50 +140,38 @@ ...@@ -192,50 +140,38 @@
192 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 140 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
193 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 141 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
194 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 142 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
195 -"GSE88980","GSM2356687","WT NaCl 1","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 143 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
196 -"GSE88980","GSM2356688","WT NaCl 2","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 144 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
197 -"GSE88980","GSM2356689","ΔompR NaCl 1","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 145 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
198 -"GSE88980","GSM2356690","ΔompR NaCl 2","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 146 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
199 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 147 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
200 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 148 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
201 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 149 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
202 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 150 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
203 -"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 151 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
204 -"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 152 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
205 -"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 153 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
206 -"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 154 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
207 -"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 155 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
208 -"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 156 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
209 -"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 157 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
210 -"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 158 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
211 -"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 159 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
212 -"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 160 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
213 -"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 161 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
214 -"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 162 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
163 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
164 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
165 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
166 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
167 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
168 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
169 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
170 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
215 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 171 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
216 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 172 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
217 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 173 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
218 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 174 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
219 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
220 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
221 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
222 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
223 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
224 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
225 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
226 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
227 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
228 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
229 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
230 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
231 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
232 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
233 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
234 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
235 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
236 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
237 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
238 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
239 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 175 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
240 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 176 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
241 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 177 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
...@@ -250,12 +186,41 @@ ...@@ -250,12 +186,41 @@
250 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 186 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
251 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 187 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
252 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 188 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
253 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 189 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
254 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 190 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
255 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 191 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
256 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 192 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
257 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 193 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
258 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 194 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
195 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
196 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
197 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
198 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
199 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
200 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
201 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
202 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
203 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
204 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
205 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
206 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
207 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
208 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
209 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
210 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
211 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
212 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
213 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
214 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
215 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
216 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
217 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
218 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
219 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
220 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
221 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
222 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
223 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
259 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 224 "GSE55199","GSM1331409","LB 0.4 B1 TEX neg L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
260 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 225 "GSE55199","GSM1331410","LB 0.4 B1 TEX pos L1 GA","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
261 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 226 "GSE55199","GSM1331411","LB 0.4 B2 TEX neg L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","LB","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
...@@ -278,3 +243,56 @@ ...@@ -278,3 +243,56 @@
278 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 243 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
279 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 244 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
280 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 245 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
246 +"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
247 +"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
248 +"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
249 +"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
250 +"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
251 +"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
252 +"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
253 +"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
254 +"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
255 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
256 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
257 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
258 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
259 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
260 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
261 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
262 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
263 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
264 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
265 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
266 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
267 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
268 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
269 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
270 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
271 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
272 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
273 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
274 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
275 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
276 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
277 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
278 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
279 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
280 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
281 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
282 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
283 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
284 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
285 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
286 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
287 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
288 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
289 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
290 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
291 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
292 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
293 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
294 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
295 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
296 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
297 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
298 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
This diff could not be displayed because it is too large.
1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit" 1 "Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
2 -"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 2 +"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
3 -"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 3 +"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
4 -"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 4 +"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
5 -"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 5 +"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
6 -"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 6 +"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
7 -"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","","" 7 +"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
8 -"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 8 +"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
9 -"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 9 +"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","",""
10 -"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 10 +"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
11 -"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","","" 11 +"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
12 -"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 12 +"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
13 -"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","","" 13 +"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","",""
14 +"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
15 +"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
16 +"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
17 +"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
18 +"GSE88980","GSM2356687","WT NaCl 1","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
19 +"GSE88980","GSM2356688","WT NaCl 2","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
20 +"GSE88980","GSM2356689","ΔompR NaCl 1","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
21 +"GSE88980","GSM2356690","ΔompR NaCl 2","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","",""
22 +"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
23 +"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
24 +"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
25 +"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
26 +"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
27 +"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
28 +"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
29 +"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
14 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 30 "GSE41186","GSM1010199","FNR - Anaerobic - A","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
15 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 31 "GSE41186","GSM1010200","FNR - Anaerobic - B","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
16 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 32 "GSE41186","GSM1010201","FNR - Anaerobic - C","Pre-cleared FNR antibody","Escherichia coli","K-12","MG1655star","WT","","","","","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
...@@ -36,114 +52,46 @@ ...@@ -36,114 +52,46 @@
36 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 52 "GSE41186","GSM1143890","HNS - Anaerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
37 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","","" 53 "GSE41186","GSM1143891","HNS - Aerobic B","Pre-cleared H-NS polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, aerobically (25% O2, 70% N2 and 5% CO2)","","","","OD600 of 0.35","mid-log phase","","",""
38 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","","" 54 "GSE41186","GSM1143892","IHF - Anaerobic B","Pre-cleared IHF polyclonal antibody","Escherichia coli","K-12","MG1655","WT","","","","","anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of 0.3","mid-log phase","","",""
39 -"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
40 -"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
41 -"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
42 -"GSE74931","GSM1937963","∆fur Anaerobic [IP vs nput]","affinity purified anti-Fur antibody","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur","","MOPS minimal glucose media","","10 µM FeSO4","","","","","","mid-log","","",""
43 -"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
44 -"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
45 -"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
46 -"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
47 -"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
48 -"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
49 -"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
50 -"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
51 -"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
52 -"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
53 -"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
54 -"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
55 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","","" 55 "GSE60546","GSM1482120","","","Escherichia coli","K-12","MG1655","","NC_000913","M9 medium","ChIP-Seq","2 g/L glucose, presence or absence of 1 g/L arginine","","37°C","","","OD600 ≈ 0.5","","","",""
56 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","","" 56 "GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
57 -"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","","" 57 +"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
58 -"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","","" 58 +"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
59 -"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","","" 59 +"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
60 -"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","","" 60 +"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
61 -"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","","" 61 +"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
62 -"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","","" 62 +"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
63 -"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","","" 63 +"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
64 -"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","","" 64 +"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
65 -"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","","" 65 +"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
66 -"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","","" 66 +"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
67 -"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","","" 67 +"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
68 -"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","","" 68 +"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
69 -"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
70 -"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
71 -"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
72 -"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
73 -"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
74 -"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
75 -"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
76 -"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
77 -"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
78 -"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
79 -"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
80 -"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
81 -"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
82 -"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
83 -"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
84 -"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
85 -"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
86 -"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
87 -"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
88 -"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
89 -"GSE66441","GSM1622463","ChIP-exo GadE pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
90 -"GSE66441","GSM1622464","ChIP-exo GadE pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadE-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
91 -"GSE66441","GSM1622465","ChIP-exo GadW pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
92 -"GSE66441","GSM1622466","ChIP-exo GadW pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadW-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
93 -"GSE66441","GSM1622467","ChIP-exo GadX pH5.5 1","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
94 -"GSE66441","GSM1622468","ChIP-exo GadX pH5.5 2","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","gadX-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
95 -"GSE66441","GSM1633277","ChIP-exo RpoS pH5.5 1","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
96 -"GSE66441","GSM1633278","ChIP-exo RpoS pH5.5 2","anti-RpoS","Escherichia coli str. K-12 substr. MG1655","","","WT","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
97 -"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
98 -"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
99 -"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
100 -"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
101 -"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
102 -"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
103 -"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
104 -"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
105 -"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
106 -"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
107 -"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
108 -"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
109 -"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
110 -"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
111 -"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
112 -"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
113 -"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
114 -"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
115 -"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
116 -"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
117 -"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
118 -"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
119 -"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
120 -"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
121 "GSE88979","GSM2356685","OmpR NaCl 1","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","","" 69 "GSE88979","GSM2356685","OmpR NaCl 1","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","",""
122 "GSE88979","GSM2356686","OmpR NaCl 2","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","","" 70 "GSE88979","GSM2356686","OmpR NaCl 2","anti-myc","Escherichia coli","K-12","MG1655","ompR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","","","","","","mid-log pahse","","",""
123 -"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 71 +"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
124 -"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 72 +"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
125 -"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 73 +"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
126 -"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 74 +"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
127 -"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 75 +"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
128 -"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 76 +"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
129 -"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 77 +"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
130 -"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm" 78 +"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
131 -"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 79 +"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
132 -"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 80 +"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
133 -"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 81 +"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
134 -"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 82 +"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","",""
135 -"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 83 +"GSE54899","GSM1326335","Fur with Fe 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
136 -"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 84 +"GSE54899","GSM1326336","Fur with Fe 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
137 -"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 85 +"GSE54899","GSM1326337","Fur with DPD 1 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
138 -"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 86 +"GSE54899","GSM1326338","Fur with DPD 2 (ChIP-exo)","anti-myc","Escherichia coli str. K-12 substr. MG1655","","","fur-8myc","NC_000913, ASM584v2, ChIP-Seq","M9 minimal media","ChIP-exo","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
139 -"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 87 +"GSE54899","GSM1326339","RpoB with Fe 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
140 -"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 88 +"GSE54899","GSM1326340","RpoB with Fe 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2, 2h","aerobically","37°C","","","","mid-log phase","","",""
141 -"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 89 +"GSE54899","GSM1326341","RpoB with Fe and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
142 -"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 90 +"GSE54899","GSM1326342","RpoB with Fe and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","Fe and rifampicin, 0.2% glucose, 0.1mM of FeCl2, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
143 -"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 91 +"GSE54899","GSM1326343","RpoB with DPD 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
144 -"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 92 +"GSE54899","GSM1326344","RpoB with DPD 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD, 0.2% glucose, 0.2mM of DPD, 2h","aerobically","37°C","","","","mid-log phase","","",""
145 -"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 93 +"GSE54899","GSM1326345","RpoB with DPD and rifampicin 1 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
146 -"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm" 94 +"GSE54899","GSM1326346","RpoB with DPD and rifampicin 2 (ChIP-exo)","anti-RpoB","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","ChIP-exo, ChIP-Seq","DPD and rifampicin, 0.2% glucose, 0.2mM of DPD, 2h, rifampicin dissolved in methanol, 150 mg/mL, 20 min","aerobically","37°C","","","","mid-log phase","","",""
147 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","","" 95 "GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
148 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","","" 96 "GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
149 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","","" 97 "GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
...@@ -192,50 +140,38 @@ ...@@ -192,50 +140,38 @@
192 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","","" 140 "GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
193 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","","" 141 "GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
194 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","","" 142 "GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
195 -"GSE88980","GSM2356687","WT NaCl 1","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 143 +"GSE4321","GSM98717","EC18n177 RpoH 0 min Time course 1, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
196 -"GSE88980","GSM2356688","WT NaCl 2","","Escherichia coli","K-12","MG1655","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 144 +"GSE4321","GSM98718","EC18n178 RpoH 2.5 min Time course 1, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
197 -"GSE88980","GSM2356689","ΔompR NaCl 1","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 145 +"GSE4321","GSM98719","EC18n179 RpoH 5 min Time course 1, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
198 -"GSE88980","GSM2356690","ΔompR NaCl 2","","Escherichia coli","K-12","MG1655","ompR deletion mutant","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose, 0.3 M of NaCl, 30 min","aerobically","37°C","","","","mid-log phase","","","" 146 +"GSE4321","GSM98720","EC18n180 RpoH 10 min Time course 1, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
199 -"GSE41190","GSM1010244","Ecoli_wild-type_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 147 +"GSE4321","GSM98721","EC18n181 RpoH 20 min Time course 1, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
200 -"GSE41190","GSM1010245","Ecoli_wild-type_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","Wild-Type","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 148 +"GSE4321","GSM98722","EC18n167 RpoH 0 min Time course 2, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
201 -"GSE41190","GSM1010246","Ecoli_dFNR_rep1_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 149 +"GSE4321","GSM98723","EC18n168 RpoH 2.5 min Time course 2, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
202 -"GSE41190","GSM1010247","Ecoli_dFNR_rep2_anaerobic","","Escherichia coli str. K-12 substr. MG1655star","K-12","","dFNR (PK4854), dFNR","U00096.2","MOPS","RNA-Seq","0.2% glucose","anaerobic, anerobically (95% N2, 5% CO2)","37°C","","","O.D.600nm 0.3","mid-log phase","","","" 150 +"GSE4321","GSM98724","EC18n169 RpoH 5 min Time course 2, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
203 -"GSE65642","GSM1602347","WT glucose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 151 +"GSE4321","GSM98725","EC18n170 RpoH 10 min Time course 2, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
204 -"GSE65642","GSM1602348","WT glucose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 152 +"GSE4321","GSM98726","EC18n171 RpoH 20 min Time course 2, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
205 -"GSE65642","GSM1602349","WT fructose 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 153 +"GSE4321","GSM98727","EC18n182 RpoH 0 min Time course 3, Wild type control (0 min), RpoH induced (0 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
206 -"GSE65642","GSM1602350","WT fructose 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 154 +"GSE4321","GSM98728","EC18n183 RpoH 2.5 min Time course 3, Wild type control (2.5 min), RpoH induced (2.5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
207 -"GSE65642","GSM1602351","WT acetate 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 155 +"GSE4321","GSM98729","EC18n184 RpoH 5 min Time course 3, Wild type control (5 min), RpoH induced (5 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
208 -"GSE65642","GSM1602352","WT acetate 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 156 +"GSE4321","GSM98730","EC18n185 RpoH 10 min Time course 3, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
209 -"GSE65642","GSM1602353","Δcra glucose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 157 +"GSE4321","GSM98731","EC18n186 RpoH 20 min Time course 3, Wild type control (20 min), RpoH induced (20 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
210 -"GSE65642","GSM1602354","Δcra glucose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","glucose, 0.2% glucose","aerobically","37°C","","","","mid-log phase","","","" 158 +"GSE4321","GSM98732","EC18n122 RpoH 10 min Time course 4, Wild type control (10 min), RpoH induced (10 min)","","Escherichia coli","","MG1655","PhtpG::lacZ delta lacX74/ptrc99A (control vector), PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH)","","M9 minimal complete media","","1 mM IPTG","aerobically","30 degrees C","","","OD450 = 0.3","","","","gyratory water bath shaking at 240 rpm"
211 -"GSE65642","GSM1602355","Δcra fructose 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 159 +"GSE65641","GSM1602341","Cra glucose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
212 -"GSE65642","GSM1602356","Δcra fructose 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","fructose, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 160 +"GSE65641","GSM1602342","Cra glucose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% glucose","aerobically","37°C","","","","mid-log","","",""
213 -"GSE65642","GSM1602357","Δcra acetate 1","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 161 +"GSE65641","GSM1602343","Cra fructose 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
214 -"GSE65642","GSM1602358","Δcra acetate 2","","Escherichia coli, K-12 MG1655","","","delta_cra","NC_000913","M9 minimal media","RNA-Seq","acetate, 0.2%","aerobically","37°C","","","","mid-log phase","","","" 162 +"GSE65641","GSM1602344","Cra fructose 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% fructose","aerobically","37°C","","","","mid-log","","",""
163 +"GSE65641","GSM1602345","Cra acetate 1","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
164 +"GSE65641","GSM1602346","Cra acetate 2","anti-myc","Escherichia coli, K-12 MG1655","","","cra-8myc-tagged","ASM584v2","M9 minimal media","ChIP-Seq","0.2% acetate","aerobically","37°C","","","","mid-log","","",""
165 +"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
166 +"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
167 +"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
168 +"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
169 +"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
170 +"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
215 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 171 "GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
216 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","","" 172 "GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
217 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 173 "GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
218 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","","" 174 "GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
219 -"GSE26054","GSM639826","ArgR_Arginine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
220 -"GSE26054","GSM639827","ArgR_Arginine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","1g/L arginine","","","","","","","","",""
221 -"GSE26054","GSM639828","ArgR_NH4Cl_1, Escherichia coli str. K-12 substr. MG1655","9E10 Myc tag","","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
222 -"GSE26054","GSM639829","ArgR_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","ArgR-8myc","","glucose (2 g/L) minimal W2 medium","","2g/L glutamine","","","","","","","","",""
223 -"GSE26054","GSM639830","Lrp_Leu_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
224 -"GSE26054","GSM639831","Lrp_Leu_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
225 -"GSE26054","GSM639832","Lrp_Leu_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
226 -"GSE26054","GSM639833","Lrp_NH4Cl_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
227 -"GSE26054","GSM639834","Lrp_NH4Cl_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
228 -"GSE26054","GSM639835","Lrp_NH4Cl_3","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","Lrp-8myc","","glucose (2 g/L) minimal M9 medium","","10 mM leucine","","","","","","","","",""
229 -"GSE26054","GSM639836","TrpR_Trp","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
230 -"GSE26054","GSM639837","TrpR_glucose","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","TrpR-8myc","","glucose (2 g/L) minimal M9 medium","","20 mg/L tryptophan","","","","","","","","",""
231 -"GSE65711","GSM1603386","WT PQ 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
232 -"GSE65711","GSM1603387","WT PQ 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
233 -"GSE65711","GSM1603388","ΔoxyR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
234 -"GSE65711","GSM1603389","ΔoxyR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-oxyR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
235 -"GSE65711","GSM1603390","ΔsoxR PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
236 -"GSE65711","GSM1603391","ΔsoxR PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxR","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
237 -"GSE65711","GSM1603392","ΔsoxS PQ 1","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
238 -"GSE65711","GSM1603393","ΔsoxS PQ 2","","Escherichia coli, K-12 MG1655","","","delta-soxS","NC_000913","M9 minimal media","RNA-Seq","250 uM of paraquat, 20 min, 0.2% glucose","aerobically","37°C","","","","mid-log pahse","","",""
239 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 175 "GSE74930","GSM1937949","Wild-type Aerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
240 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 176 "GSE74930","GSM1937950","Wild-type Aerobic B","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
241 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 177 "GSE74930","GSM1937951","Wild-type Anaerobic A","","Escherichia coli str. K-12 substr. MG1655","","","wild type","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
...@@ -250,12 +186,41 @@ ...@@ -250,12 +186,41 @@
250 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 186 "GSE74930","GSM1937960","∆fur ∆ryhB Anaerobic B","","Escherichia coli str. K-12 substr. MG1655","","","lacking the transcription factor Fur and the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
251 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 187 "GSE74930","GSM1937961","∆ryhB Aerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
252 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","","" 188 "GSE74930","GSM1937962","∆ryhB Anaerobic","","Escherichia coli str. K-12 substr. MG1655","","","lacking the small RNA RyhB","","MOPS minimal glucose media","","10 µM FeSO4","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log phase","","",""
253 -"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 189 +"GSE19053","GSM471482","RNAP old rep1","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
254 -"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 190 +"GSE19053","GSM471483","RNAP old rep2","RNA polymerase subunit β","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
255 -"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 191 +"GSE19053","GSM471484","SeqA old rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
256 -"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 192 +"GSE19053","GSM471485","SeqA old rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
257 -"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 193 +"GSE19053","GSM471486","SeqA new rep1","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
258 -"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","","" 194 +"GSE19053","GSM471487","SeqA new rep2","SeqA","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
195 +"GSE19053","GSM471488","SeqA old deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
196 +"GSE19053","GSM471489","SeqA new deltaSeqA","SeqA","Escherichia coli str. K-12 substr. MG1655","","","ΔseqA","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
197 +"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
198 +"GSE19053","GSM471491","σ32 43°C rep1, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
199 +"GSE19053","GSM471492","σ32 43°C rep2, σ32 ChIP DNA, heat","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
200 +"GSE19053","GSM471493","σ32 30°C rep1, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
201 +"GSE19053","GSM471494","σ32 30°C rep2, σ32 ChIP DNA, control","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
202 +"GSE19053","GSM471495","σ32 30°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C (see heat sample), 30 °C","","","OD600 of about 0.3","","","flask",""
203 +"GSE19053","GSM476145","σ32 43°C short RNase","σ32","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","","","","","43 °C, 30 °C (see control sample)","","","OD600 of about 0.3","","","flask",""
204 +"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
205 +"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
206 +"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
207 +"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
208 +"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
209 +"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
210 +"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
211 +"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
212 +"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
213 +"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
214 +"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
215 +"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
216 +"GSE54901","GSM1326347","WT with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
217 +"GSE54901","GSM1326348","WT with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
218 +"GSE54901","GSM1326349","WT with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
219 +"GSE54901","GSM1326350","WT with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","WT","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
220 +"GSE54901","GSM1326351","Δfur with Fe 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
221 +"GSE54901","GSM1326352","Δfur with Fe 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","Fe, 0.2% glucose, 0.1mM of FeCl2","aerobically","37°C","","","","mid-log phase","","",""
222 +"GSE54901","GSM1326353","Δfur with DPD 1 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
223 +"GSE54901","GSM1326354","Δfur with DPD 2 (RNA-seq)","","Escherichia coli str. K-12 substr. MG1655","","","Δfur","NC_000913, ASM584v2","M9 minimal media","RNA-Seq","DPD, 0.2% glucose, 0.2mM of DPD","aerobically","37°C","","","","mid-log phase","","",""
259 "GSE93506","GSM2453482","CsiR_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","","" 224 "GSE93506","GSM2453482","CsiR_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","",""
260 "GSE93506","GSM2453483","Nac_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","","" 225 "GSE93506","GSM2453483","Nac_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","",""
261 "GSE93506","GSM2453484","NtrC_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","","" 226 "GSE93506","GSM2453484","NtrC_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","",""
...@@ -289,3 +254,56 @@ ...@@ -289,3 +254,56 @@
289 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 254 "GSE55199","GSM1331428","M63 0.4 B2 TEX neg L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
290 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 255 "GSE55199","GSM1331429","M63 0.4 B2 TEX pos L1 HS1","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
291 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","","" 256 "GSE55199","GSM1331430","M63 0.4 B2 TEX pos L1 HS2","","Escherichia coli str. K-12 substr. MG1655","","","wild type","NC_000913.2","M63, M63 minimal glucose","RNA-Seq","","","","","","OD600 of ~0.4","exponential","","",""
257 +"GSE74932","GSM1937964","Fur IP ChIP-Seq Aerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
258 +"GSE74932","GSM1937965","Fur IP ChIP-Seq Aerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
259 +"GSE74932","GSM1937966","Fur IP ChIP-Seq Aerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Aerobic, aerobically (70% N2, 25% O2, and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
260 +"GSE74932","GSM1937967","Fur IP ChIP-Seq Anaerobic A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
261 +"GSE74932","GSM1937968","Fur IP ChIP-Seq Anaerobic B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
262 +"GSE74932","GSM1937969","Fur IP ChIP-Seq Anaerobic C","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","Wild-type","U00096.2","MOPS minimal glucose media","ChIP-Seq","10 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","Anaerobic, anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
263 +"GSE74932","GSM1937970","Fur IP ChIP-Seq Anaerobic, Iron Deficient A","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
264 +"GSE74932","GSM1937971","Fur IP ChIP-Seq Anaerobic, Iron Deficient B","anti-Fur polyclonal antibody","Escherichia coli str. K-12 substr. MG1655","","","{delta}tonB, {delta}feoA, {delta}zupT K12","U00096.2","MOPS minimal glucose media","ChIP-Seq","1 µM FeSO4, Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","anaerobically (95% N2 and 5% CO2)","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
265 +"GSE74932","GSM1937972","Input ChIP-Seq","none","Escherichia coli str. K-12 substr. MG1655","","","Combined input","U00096.2","","ChIP-Seq","Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)","","","","","OD600 of ~0.3-0.35","mid-log, mid-log phase","","",""
266 +"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
267 +"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
268 +"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
269 +"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
270 +"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
271 +"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
272 +"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
273 +"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
274 +"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
275 +"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
276 +"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
277 +"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
278 +"GSE66481","GSM1623160","WT pH5.5 1","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
279 +"GSE66481","GSM1623161","WT pH5.5 2","","Escherichia coli, K-12 MG1655","","","WT","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
280 +"GSE66481","GSM1623162","ΔgadE pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
281 +"GSE66481","GSM1623163","ΔgadE pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadE","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
282 +"GSE66481","GSM1623164","ΔgadW pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
283 +"GSE66481","GSM1623165","ΔgadW pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadW","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
284 +"GSE66481","GSM1623166","ΔgadX pH5.5 1","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
285 +"GSE66481","GSM1623167","ΔgadX pH5.5 2","","Escherichia coli, K-12 MG1655","","","delta-gadX","NC_000913","M9 minimal media","RNA-Seq","0.2% glucose","aerobically","37°C","pH 5.5","","OD600 = 0.3","mid-log phase","","","250 rpm"
286 +"GSE65710","GSM1603380","OxyR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
287 +"GSE65710","GSM1603381","OxyR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","oxyR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
288 +"GSE65710","GSM1603382","SoxR PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
289 +"GSE65710","GSM1603383","SoxR PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxR-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
290 +"GSE65710","GSM1603384","SoxS PQ 1","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
291 +"GSE65710","GSM1603385","SoxS PQ 2","anti-myc","Escherichia coli, K-12 MG1655","","","soxS-8myc","ASM584v2","M9 minimal media","ChIP-Seq","250 uM of paraquat, 20 min, 0.2% glucose","","","","","","mid-log phase","","",""
292 +"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
293 +"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
294 +"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
295 +"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
296 +"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
297 +"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
298 +"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
299 +"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
300 +"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
301 +"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
302 +"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
303 +"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
304 +"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
305 +"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
306 +"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
307 +"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
308 +"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
309 +"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
1 +Serie Sample
2 +GSE11230 GSM282644
3 +GSE11230 GSM282645
4 +GSE11230 GSM283059
5 +GSE19053 GSM471482
6 +GSE19053 GSM471483
7 +GSE19053 GSM471484
8 +GSE19053 GSM471485
9 +GSE19053 GSM471486
10 +GSE19053 GSM471487
11 +GSE19053 GSM471488
12 +GSE19053 GSM471489
13 +GSE19053 GSM471490
14 +GSE19053 GSM471491
15 +GSE19053 GSM471492
16 +GSE19053 GSM471493
17 +GSE19053 GSM471494
18 +GSE19053 GSM471495
19 +GSE19053 GSM476145
20 +GSE26054 GSM639826
21 +GSE26054 GSM639827
22 +GSE26054 GSM639828
23 +GSE26054 GSM639829
24 +GSE26054 GSM639830
25 +GSE26054 GSM639831
26 +GSE26054 GSM639832
27 +GSE26054 GSM639833
28 +GSE26054 GSM639834
29 +GSE26054 GSM639835
30 +GSE26054 GSM639836
31 +GSE26054 GSM639837
32 +GSE26589 GSM654485
33 +GSE26589 GSM654486
34 +GSE26589 GSM654487
35 +GSE26589 GSM654488
36 +GSE41186 GSM1010199
37 +GSE41186 GSM1010200
38 +GSE41186 GSM1010201
39 +GSE41186 GSM1010202
40 +GSE41186 GSM1010203
41 +GSE41186 GSM1010204
42 +GSE41186 GSM1010205
43 +GSE41186 GSM1010206
44 +GSE41186 GSM1010207
45 +GSE41186 GSM1010208
46 +GSE41186 GSM1010209
47 +GSE41186 GSM1010210
48 +GSE41186 GSM1010211
49 +GSE41186 GSM1010212
50 +GSE41186 GSM1010213
51 +GSE41186 GSM1010214
52 +GSE41186 GSM1010215
53 +GSE41186 GSM1010216
54 +GSE41186 GSM1010217
55 +GSE41186 GSM1010218
56 +GSE41186 GSM1054383
57 +GSE41186 GSM1054384
58 +GSE41186 GSM1143890
59 +GSE41186 GSM1143891
60 +GSE41186 GSM1143892
61 +GSE41190 GSM1010244
62 +GSE41190 GSM1010245
63 +GSE41190 GSM1010246
64 +GSE41190 GSM1010247
65 +GSE41195 GSM1010199
66 +GSE41195 GSM1010200
67 +GSE41195 GSM1010201
68 +GSE41195 GSM1010202
69 +GSE41195 GSM1010203
70 +GSE41195 GSM1010204
71 +GSE41195 GSM1010205
72 +GSE41195 GSM1010206
73 +GSE41195 GSM1010207
74 +GSE41195 GSM1010208
75 +GSE41195 GSM1010209
76 +GSE41195 GSM1010210
77 +GSE41195 GSM1010211
78 +GSE41195 GSM1010212
79 +GSE41195 GSM1010213
80 +GSE41195 GSM1010214
81 +GSE41195 GSM1010215
82 +GSE41195 GSM1010216
83 +GSE41195 GSM1010217
84 +GSE41195 GSM1010218
85 +GSE41195 GSM1010219
86 +GSE41195 GSM1010220
87 +GSE41195 GSM1010221
88 +GSE41195 GSM1010222
89 +GSE41195 GSM1010223
90 +GSE41195 GSM1010224
91 +GSE41195 GSM1010240
92 +GSE41195 GSM1010241
93 +GSE41195 GSM1010242
94 +GSE41195 GSM1010243
95 +GSE41195 GSM1010244
96 +GSE41195 GSM1010245
97 +GSE41195 GSM1010246
98 +GSE41195 GSM1010247
99 +GSE41195 GSM1054383
100 +GSE41195 GSM1054384
101 +GSE41195 GSM1072326
102 +GSE41195 GSM1072327
103 +GSE41195 GSM1072328
104 +GSE41195 GSM1124977
105 +GSE41195 GSM1124978
106 +GSE41195 GSM1124979
107 +GSE41195 GSM1124980
108 +GSE41195 GSM1126445
109 +GSE41195 GSM1126446
110 +GSE41195 GSM1143890
111 +GSE41195 GSM1143891
112 +GSE41195 GSM1143892
113 +GSE4321 GSM98717
114 +GSE4321 GSM98718
115 +GSE4321 GSM98719
116 +GSE4321 GSM98720
117 +GSE4321 GSM98721
118 +GSE4321 GSM98722
119 +GSE4321 GSM98723
120 +GSE4321 GSM98724
121 +GSE4321 GSM98725
122 +GSE4321 GSM98726
123 +GSE4321 GSM98727
124 +GSE4321 GSM98728
125 +GSE4321 GSM98729
126 +GSE4321 GSM98730
127 +GSE4321 GSM98731
128 +GSE4321 GSM98732
129 +GSE54899 GSM1326335
130 +GSE54899 GSM1326336
131 +GSE54899 GSM1326337
132 +GSE54899 GSM1326338
133 +GSE54899 GSM1326339
134 +GSE54899 GSM1326340
135 +GSE54899 GSM1326341
136 +GSE54899 GSM1326342
137 +GSE54899 GSM1326343
138 +GSE54899 GSM1326344
139 +GSE54899 GSM1326345
140 +GSE54899 GSM1326346
141 +GSE54901 GSM1326335
142 +GSE54901 GSM1326336
143 +GSE54901 GSM1326337
144 +GSE54901 GSM1326338
145 +GSE54901 GSM1326339
146 +GSE54901 GSM1326340
147 +GSE54901 GSM1326341
148 +GSE54901 GSM1326342
149 +GSE54901 GSM1326343
150 +GSE54901 GSM1326344
151 +GSE54901 GSM1326345
152 +GSE54901 GSM1326346
153 +GSE54901 GSM1326347
154 +GSE54901 GSM1326348
155 +GSE54901 GSM1326349
156 +GSE54901 GSM1326350
157 +GSE54901 GSM1326351
158 +GSE54901 GSM1326352
159 +GSE54901 GSM1326353
160 +GSE54901 GSM1326354
161 +GSE55199 GSM1331409
162 +GSE55199 GSM1331410
163 +GSE55199 GSM1331411
164 +GSE55199 GSM1331412
165 +GSE55199 GSM1331413
166 +GSE55199 GSM1331414
167 +GSE55199 GSM1331415
168 +GSE55199 GSM1331416
169 +GSE55199 GSM1331417
170 +GSE55199 GSM1331418
171 +GSE55199 GSM1331419
172 +GSE55199 GSM1331420
173 +GSE55199 GSM1331421
174 +GSE55199 GSM1331422
175 +GSE55199 GSM1331423
176 +GSE55199 GSM1331424
177 +GSE55199 GSM1331425
178 +GSE55199 GSM1331426
179 +GSE55199 GSM1331427
180 +GSE55199 GSM1331428
181 +GSE55199 GSM1331429
182 +GSE55199 GSM1331430
183 +GSE55365 GSM1334746
184 +GSE55365 GSM1334747
185 +GSE55365 GSM1334748
186 +GSE55365 GSM1334749
187 +GSE55365 GSM1334750
188 +GSE55365 GSM1334751
189 +GSE55365 GSM1334752
190 +GSE55365 GSM1334753
191 +GSE55365 GSM1334754
192 +GSE55365 GSM1334755
193 +GSE55365 GSM1334756
194 +GSE55365 GSM1334757
195 +GSE55365 GSM1334758
196 +GSE55365 GSM1334759
197 +GSE55365 GSM1334760
198 +GSE55365 GSM1334761
199 +GSE55365 GSM1334762
200 +GSE55365 GSM1334763
201 +GSE55366 GSM1334764
202 +GSE55366 GSM1334765
203 +GSE55366 GSM1334766
204 +GSE55366 GSM1334767
205 +GSE55366 GSM1334768
206 +GSE55366 GSM1334769
207 +GSE55366 GSM1334770
208 +GSE55366 GSM1334771
209 +GSE55366 GSM1334772
210 +GSE55366 GSM1334773
211 +GSE55366 GSM1334774
212 +GSE55366 GSM1334775
213 +GSE60546 GSM1482120
214 +GSE60546 GSM1482121
215 +GSE65641 GSM1602341
216 +GSE65641 GSM1602342
217 +GSE65641 GSM1602343
218 +GSE65641 GSM1602344
219 +GSE65641 GSM1602345
220 +GSE65641 GSM1602346
221 +GSE65641 GSM2829281
222 +GSE65641 GSM2829282
223 +GSE65641 GSM2829283
224 +GSE65641 GSM2829284
225 +GSE65641 GSM2829285
226 +GSE65641 GSM2829286
227 +GSE65642 GSM1602347
228 +GSE65642 GSM1602348
229 +GSE65642 GSM1602349
230 +GSE65642 GSM1602350
231 +GSE65642 GSM1602351
232 +GSE65642 GSM1602352
233 +GSE65642 GSM1602353
234 +GSE65642 GSM1602354
235 +GSE65642 GSM1602355
236 +GSE65642 GSM1602356
237 +GSE65642 GSM1602357
238 +GSE65642 GSM1602358
239 +GSE65710 GSM1603380
240 +GSE65710 GSM1603381
241 +GSE65710 GSM1603382
242 +GSE65710 GSM1603383
243 +GSE65710 GSM1603384
244 +GSE65710 GSM1603385
245 +GSE65711 GSM1603386
246 +GSE65711 GSM1603387
247 +GSE65711 GSM1603388
248 +GSE65711 GSM1603389
249 +GSE65711 GSM1603390
250 +GSE65711 GSM1603391
251 +GSE65711 GSM1603392
252 +GSE65711 GSM1603393
253 +GSE66441 GSM1622463
254 +GSE66441 GSM1622464
255 +GSE66441 GSM1622465
256 +GSE66441 GSM1622466
257 +GSE66441 GSM1622467
258 +GSE66441 GSM1622468
259 +GSE66441 GSM1633277
260 +GSE66441 GSM1633278
261 +GSE66481 GSM1623160
262 +GSE66481 GSM1623161
263 +GSE66481 GSM1623162
264 +GSE66481 GSM1623163
265 +GSE66481 GSM1623164
266 +GSE66481 GSM1623165
267 +GSE66481 GSM1623166
268 +GSE66481 GSM1623167
269 +GSE74930 GSM1937949
270 +GSE74930 GSM1937950
271 +GSE74930 GSM1937951
272 +GSE74930 GSM1937952
273 +GSE74930 GSM1937953
274 +GSE74930 GSM1937954
275 +GSE74930 GSM1937955
276 +GSE74930 GSM1937956
277 +GSE74930 GSM1937957
278 +GSE74930 GSM1937958
279 +GSE74930 GSM1937959
280 +GSE74930 GSM1937960
281 +GSE74930 GSM1937961
282 +GSE74930 GSM1937962
283 +GSE74931 GSM1937963
284 +GSE74932 GSM1937964
285 +GSE74932 GSM1937965
286 +GSE74932 GSM1937966
287 +GSE74932 GSM1937967
288 +GSE74932 GSM1937968
289 +GSE74932 GSM1937969
290 +GSE74932 GSM1937970
291 +GSE74932 GSM1937971
292 +GSE74932 GSM1937972
293 +GSE88979 GSM2356685
294 +GSE88979 GSM2356686
295 +GSE88980 GSM2356687
296 +GSE88980 GSM2356688
297 +GSE88980 GSM2356689
298 +GSE88980 GSM2356690
299 +GSE93506 GSM2453482
300 +GSE93506 GSM2453483
301 +GSE93506 GSM2453484
302 +GSE93506 GSM2453485
303 +GSE93506 GSM2453486
304 +GSE93506 GSM2453487
305 +GSE93506 GSM2667742
306 +GSE93506 GSM2667743
307 +GSE93506 GSM2667744
308 +GSE93506 GSM2667745
309 +GSE93506 GSM2667746
...@@ -57,6 +57,7 @@ if __name__ == "__main__": ...@@ -57,6 +57,7 @@ if __name__ == "__main__":
57 tags = ["Name", "Anti", "Orgn", "Strain", "Substrain", "Gtype", "Gversion", "Med", "Technique", "Supp", "Air", "Temp", "pH", "Press", "OD", "Phase", "Rate", "Vess", "Agit", ] 57 tags = ["Name", "Anti", "Orgn", "Strain", "Substrain", "Gtype", "Gversion", "Med", "Technique", "Supp", "Air", "Temp", "pH", "Press", "OD", "Phase", "Rate", "Vess", "Agit", ]
58 processed_files = 0 58 processed_files = 0
59 saved_files = 0 59 saved_files = 0
60 + complete_report = []
60 # Walk directory to read files 61 # Walk directory to read files
61 for path, dirs, files in os.walk(options.inputPath): 62 for path, dirs, files in os.walk(options.inputPath):
62 for f in files: 63 for f in files:
...@@ -119,6 +120,7 @@ if __name__ == "__main__": ...@@ -119,6 +120,7 @@ if __name__ == "__main__":
119 output = output + '"' + tag + '",' 120 output = output + '"' + tag + '",'
120 output = output.rstrip(',') 121 output = output.rstrip(',')
121 oFile.write(output + "\n") 122 oFile.write(output + "\n")
123 + complete_report.append(output)
122 for serie, hashSample in hashGcs.items(): 124 for serie, hashSample in hashGcs.items():
123 print("Serie: {}".format(serie)) 125 print("Serie: {}".format(serie))
124 for sample, hashTag in sorted(hashSample.items()): 126 for sample, hashTag in sorted(hashSample.items()):
...@@ -135,6 +137,7 @@ if __name__ == "__main__": ...@@ -135,6 +137,7 @@ if __name__ == "__main__":
135 output = output + '"' + tag + '",' 137 output = output + '"' + tag + '",'
136 output = output.rstrip(',') 138 output = output.rstrip(',')
137 oFile.write(output + "\n") 139 oFile.write(output + "\n")
140 + complete_report.append(output)
138 # oFile.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(sample, serie, Technique, Orgn, Strain, Substrain, Gversion, Gtype, Phase, Air, Med, Temp, Supp)) 141 # oFile.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(sample, serie, Technique, Orgn, Strain, Substrain, Gversion, Gtype, Phase, Air, Med, Temp, Supp))
139 # for tag, listContent in sorted(hashTag.items()): 142 # for tag, listContent in sorted(hashTag.items()):
140 # print("\t\tTag: {}".format(tag)) 143 # print("\t\tTag: {}".format(tag))
...@@ -144,6 +147,10 @@ if __name__ == "__main__": ...@@ -144,6 +147,10 @@ if __name__ == "__main__":
144 # oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content)) 147 # oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content))
145 saved_files+=1 148 saved_files+=1
146 149
150 + with open(os.path.join(options.outputPath, f.replace(".xml", ".complete-report.csv")), "w") as oFile:
151 + for line in complete_report:
152 + oFile.write(line + "\n")
153 +
147 print("Processed files: {}".format(processed_files)) 154 print("Processed files: {}".format(processed_files))
148 print("Saved files: {}".format(saved_files)) 155 print("Saved files: {}".format(saved_files))
149 156
......