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
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
......@@ -14,10 +18,6 @@
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
......@@ -14,10 +43,6 @@
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","",""
"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","","","",""
"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 @@
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","",""
"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","","","",""
"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 @@
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -71,25 +82,6 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","",""
"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","","","",""
"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 @@
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -71,25 +104,6 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","",""
"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","","","",""
"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 @@
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010202","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010203","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010204","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010205","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010206","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010207","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010208","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010209","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010210","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010211","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010212","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010213","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010214","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010215","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010216","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010217","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010218","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010219","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010220","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010221","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010222","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010223","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010224","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010240","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010241","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010242","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010243","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010244","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010245","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010246","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010247","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1054383","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1054384","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1072326","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1072327","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1072328","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1124977","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1124978","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1124979","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1124980","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1126445","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1126446","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -97,34 +74,41 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -145,6 +129,28 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -97,34 +74,41 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -147,6 +131,28 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -109,34 +74,53 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -159,6 +143,28 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -121,34 +86,53 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -171,6 +155,28 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -127,34 +86,59 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -177,6 +161,28 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -135,34 +86,59 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -185,6 +161,28 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -135,34 +86,59 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -143,34 +86,59 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -157,34 +86,73 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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 @@
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -158,42 +134,67 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
......@@ -214,33 +215,6 @@
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -190,46 +134,38 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -192,46 +136,38 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -192,50 +140,38 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
This diff could not be displayed because it is too large.
"Serie","Sample","Name","Anti","Orgn","Strain","Substrain","Gtype","Gversion","Med","Technique","Supp","Air","Temp","pH","Press","OD","Phase","Rate","Vess","Agit"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"GSE11230","GSM282644","NsrR_Flagtag_rep2","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM282645","NsrR_Flagtag_rep3","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"GSE11230","GSM283059","NsrR_Flagtag_rep1","","Escherichia coli","","","NsrR, Flag-tag","","L broth","","glucose, nitrate","anaerobically","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"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","","","",""
"GSE60546","GSM1482121","","","Escherichia coli","K-12","MG1655","","NC_000913","","ChIP-Seq","absence of 1 g/L arginine","","","","","","","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE41195","GSM1010199","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010200","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1010201","","","","","","","","","","","","","","","","","","",""
......@@ -192,50 +140,38 @@
"GSE41195","GSM1143890","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143891","","","","","","","","","","","","","","","","","","",""
"GSE41195","GSM1143892","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE65641","GSM2829281","RpoB WT 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829282","RpoB WT 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","Wildtype","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829283","RpoB ∆cra 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829284","RpoB ∆cra 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","cra Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829285","RpoB ∆crp 1","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE65641","GSM2829286","RpoB ∆crp 2","anti-rpoB","Escherichia coli, K-12 MG1655","","","crp Knock-out strain","ASM584v2","","ChIP-Seq","acetate","","","","","","","","",""
"GSE26589","GSM654485","PurR_Adenine_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654486","PurR_Adenine_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","Adenine, 100ug/L adenine","","","","","","","","",""
"GSE26589","GSM654487","PurR_glucose_1","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"GSE26589","GSM654488","PurR_glucose_2","9E10 Myc tag","Escherichia coli str. K-12 substr. MG1655","","","PurR-8myc","","M9 minimal medium","","glucose","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"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","","","",""
"GSE19053","GSM471490","Crosslink","","Escherichia coli str. K-12 substr. MG1655","","","wildtype","","LB","","0.2% glucose","","37 °C","","","OD600 of about 0.15","","","",""
"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",""
"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",""
"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",""
"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",""
"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",""
"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",""
"GSE54901","GSM1326335","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326336","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326337","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326338","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326339","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326340","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326341","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326342","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326343","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326344","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326345","","","","","","","","","","","","","","","","","","",""
"GSE54901","GSM1326346","","","","","","","","","","","","","","","","","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE93506","GSM2453482","CsiR_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","",""
"GSE93506","GSM2453483","Nac_ChIPSeq","anti-FLAG mAb","Escherichia coli K-12, MG1655","","","","U00096.2","LB media","ChIP-Seq","1mM IPTG, 2 hours","","37 °C","","","","","","",""
"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 @@
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55366","GSM1334764","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334765","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334766","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334767","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334768","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334769","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334770","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334771","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334772","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334773","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334774","","","","","","","","","","","","","","","","","","",""
"GSE55366","GSM1334775","","","","","","","","","","","","","","","","","","",""
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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"
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"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","","",""
"GSE55365","GSM1334746","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334747","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334748","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334749","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334750","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334751","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334752","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334753","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334754","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334755","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334756","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334757","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334758","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334759","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334760","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334761","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334762","","","","","","","","","","","","","","","","","","",""
"GSE55365","GSM1334763","","","","","","","","","","","","","","","","","","",""
......
Serie Sample
GSE11230 GSM282644
GSE11230 GSM282645
GSE11230 GSM283059
GSE19053 GSM471482
GSE19053 GSM471483
GSE19053 GSM471484
GSE19053 GSM471485
GSE19053 GSM471486
GSE19053 GSM471487
GSE19053 GSM471488
GSE19053 GSM471489
GSE19053 GSM471490
GSE19053 GSM471491
GSE19053 GSM471492
GSE19053 GSM471493
GSE19053 GSM471494
GSE19053 GSM471495
GSE19053 GSM476145
GSE26054 GSM639826
GSE26054 GSM639827
GSE26054 GSM639828
GSE26054 GSM639829
GSE26054 GSM639830
GSE26054 GSM639831
GSE26054 GSM639832
GSE26054 GSM639833
GSE26054 GSM639834
GSE26054 GSM639835
GSE26054 GSM639836
GSE26054 GSM639837
GSE26589 GSM654485
GSE26589 GSM654486
GSE26589 GSM654487
GSE26589 GSM654488
GSE41186 GSM1010199
GSE41186 GSM1010200
GSE41186 GSM1010201
GSE41186 GSM1010202
GSE41186 GSM1010203
GSE41186 GSM1010204
GSE41186 GSM1010205
GSE41186 GSM1010206
GSE41186 GSM1010207
GSE41186 GSM1010208
GSE41186 GSM1010209
GSE41186 GSM1010210
GSE41186 GSM1010211
GSE41186 GSM1010212
GSE41186 GSM1010213
GSE41186 GSM1010214
GSE41186 GSM1010215
GSE41186 GSM1010216
GSE41186 GSM1010217
GSE41186 GSM1010218
GSE41186 GSM1054383
GSE41186 GSM1054384
GSE41186 GSM1143890
GSE41186 GSM1143891
GSE41186 GSM1143892
GSE41190 GSM1010244
GSE41190 GSM1010245
GSE41190 GSM1010246
GSE41190 GSM1010247
GSE41195 GSM1010199
GSE41195 GSM1010200
GSE41195 GSM1010201
GSE41195 GSM1010202
GSE41195 GSM1010203
GSE41195 GSM1010204
GSE41195 GSM1010205
GSE41195 GSM1010206
GSE41195 GSM1010207
GSE41195 GSM1010208
GSE41195 GSM1010209
GSE41195 GSM1010210
GSE41195 GSM1010211
GSE41195 GSM1010212
GSE41195 GSM1010213
GSE41195 GSM1010214
GSE41195 GSM1010215
GSE41195 GSM1010216
GSE41195 GSM1010217
GSE41195 GSM1010218
GSE41195 GSM1010219
GSE41195 GSM1010220
GSE41195 GSM1010221
GSE41195 GSM1010222
GSE41195 GSM1010223
GSE41195 GSM1010224
GSE41195 GSM1010240
GSE41195 GSM1010241
GSE41195 GSM1010242
GSE41195 GSM1010243
GSE41195 GSM1010244
GSE41195 GSM1010245
GSE41195 GSM1010246
GSE41195 GSM1010247
GSE41195 GSM1054383
GSE41195 GSM1054384
GSE41195 GSM1072326
GSE41195 GSM1072327
GSE41195 GSM1072328
GSE41195 GSM1124977
GSE41195 GSM1124978
GSE41195 GSM1124979
GSE41195 GSM1124980
GSE41195 GSM1126445
GSE41195 GSM1126446
GSE41195 GSM1143890
GSE41195 GSM1143891
GSE41195 GSM1143892
GSE4321 GSM98717
GSE4321 GSM98718
GSE4321 GSM98719
GSE4321 GSM98720
GSE4321 GSM98721
GSE4321 GSM98722
GSE4321 GSM98723
GSE4321 GSM98724
GSE4321 GSM98725
GSE4321 GSM98726
GSE4321 GSM98727
GSE4321 GSM98728
GSE4321 GSM98729
GSE4321 GSM98730
GSE4321 GSM98731
GSE4321 GSM98732
GSE54899 GSM1326335
GSE54899 GSM1326336
GSE54899 GSM1326337
GSE54899 GSM1326338
GSE54899 GSM1326339
GSE54899 GSM1326340
GSE54899 GSM1326341
GSE54899 GSM1326342
GSE54899 GSM1326343
GSE54899 GSM1326344
GSE54899 GSM1326345
GSE54899 GSM1326346
GSE54901 GSM1326335
GSE54901 GSM1326336
GSE54901 GSM1326337
GSE54901 GSM1326338
GSE54901 GSM1326339
GSE54901 GSM1326340
GSE54901 GSM1326341
GSE54901 GSM1326342
GSE54901 GSM1326343
GSE54901 GSM1326344
GSE54901 GSM1326345
GSE54901 GSM1326346
GSE54901 GSM1326347
GSE54901 GSM1326348
GSE54901 GSM1326349
GSE54901 GSM1326350
GSE54901 GSM1326351
GSE54901 GSM1326352
GSE54901 GSM1326353
GSE54901 GSM1326354
GSE55199 GSM1331409
GSE55199 GSM1331410
GSE55199 GSM1331411
GSE55199 GSM1331412
GSE55199 GSM1331413
GSE55199 GSM1331414
GSE55199 GSM1331415
GSE55199 GSM1331416
GSE55199 GSM1331417
GSE55199 GSM1331418
GSE55199 GSM1331419
GSE55199 GSM1331420
GSE55199 GSM1331421
GSE55199 GSM1331422
GSE55199 GSM1331423
GSE55199 GSM1331424
GSE55199 GSM1331425
GSE55199 GSM1331426
GSE55199 GSM1331427
GSE55199 GSM1331428
GSE55199 GSM1331429
GSE55199 GSM1331430
GSE55365 GSM1334746
GSE55365 GSM1334747
GSE55365 GSM1334748
GSE55365 GSM1334749
GSE55365 GSM1334750
GSE55365 GSM1334751
GSE55365 GSM1334752
GSE55365 GSM1334753
GSE55365 GSM1334754
GSE55365 GSM1334755
GSE55365 GSM1334756
GSE55365 GSM1334757
GSE55365 GSM1334758
GSE55365 GSM1334759
GSE55365 GSM1334760
GSE55365 GSM1334761
GSE55365 GSM1334762
GSE55365 GSM1334763
GSE55366 GSM1334764
GSE55366 GSM1334765
GSE55366 GSM1334766
GSE55366 GSM1334767
GSE55366 GSM1334768
GSE55366 GSM1334769
GSE55366 GSM1334770
GSE55366 GSM1334771
GSE55366 GSM1334772
GSE55366 GSM1334773
GSE55366 GSM1334774
GSE55366 GSM1334775
GSE60546 GSM1482120
GSE60546 GSM1482121
GSE65641 GSM1602341
GSE65641 GSM1602342
GSE65641 GSM1602343
GSE65641 GSM1602344
GSE65641 GSM1602345
GSE65641 GSM1602346
GSE65641 GSM2829281
GSE65641 GSM2829282
GSE65641 GSM2829283
GSE65641 GSM2829284
GSE65641 GSM2829285
GSE65641 GSM2829286
GSE65642 GSM1602347
GSE65642 GSM1602348
GSE65642 GSM1602349
GSE65642 GSM1602350
GSE65642 GSM1602351
GSE65642 GSM1602352
GSE65642 GSM1602353
GSE65642 GSM1602354
GSE65642 GSM1602355
GSE65642 GSM1602356
GSE65642 GSM1602357
GSE65642 GSM1602358
GSE65710 GSM1603380
GSE65710 GSM1603381
GSE65710 GSM1603382
GSE65710 GSM1603383
GSE65710 GSM1603384
GSE65710 GSM1603385
GSE65711 GSM1603386
GSE65711 GSM1603387
GSE65711 GSM1603388
GSE65711 GSM1603389
GSE65711 GSM1603390
GSE65711 GSM1603391
GSE65711 GSM1603392
GSE65711 GSM1603393
GSE66441 GSM1622463
GSE66441 GSM1622464
GSE66441 GSM1622465
GSE66441 GSM1622466
GSE66441 GSM1622467
GSE66441 GSM1622468
GSE66441 GSM1633277
GSE66441 GSM1633278
GSE66481 GSM1623160
GSE66481 GSM1623161
GSE66481 GSM1623162
GSE66481 GSM1623163
GSE66481 GSM1623164
GSE66481 GSM1623165
GSE66481 GSM1623166
GSE66481 GSM1623167
GSE74930 GSM1937949
GSE74930 GSM1937950
GSE74930 GSM1937951
GSE74930 GSM1937952
GSE74930 GSM1937953
GSE74930 GSM1937954
GSE74930 GSM1937955
GSE74930 GSM1937956
GSE74930 GSM1937957
GSE74930 GSM1937958
GSE74930 GSM1937959
GSE74930 GSM1937960
GSE74930 GSM1937961
GSE74930 GSM1937962
GSE74931 GSM1937963
GSE74932 GSM1937964
GSE74932 GSM1937965
GSE74932 GSM1937966
GSE74932 GSM1937967
GSE74932 GSM1937968
GSE74932 GSM1937969
GSE74932 GSM1937970
GSE74932 GSM1937971
GSE74932 GSM1937972
GSE88979 GSM2356685
GSE88979 GSM2356686
GSE88980 GSM2356687
GSE88980 GSM2356688
GSE88980 GSM2356689
GSE88980 GSM2356690
GSE93506 GSM2453482
GSE93506 GSM2453483
GSE93506 GSM2453484
GSE93506 GSM2453485
GSE93506 GSM2453486
GSE93506 GSM2453487
GSE93506 GSM2667742
GSE93506 GSM2667743
GSE93506 GSM2667744
GSE93506 GSM2667745
GSE93506 GSM2667746
......@@ -57,6 +57,7 @@ if __name__ == "__main__":
tags = ["Name", "Anti", "Orgn", "Strain", "Substrain", "Gtype", "Gversion", "Med", "Technique", "Supp", "Air", "Temp", "pH", "Press", "OD", "Phase", "Rate", "Vess", "Agit", ]
processed_files = 0
saved_files = 0
complete_report = []
# Walk directory to read files
for path, dirs, files in os.walk(options.inputPath):
for f in files:
......@@ -119,6 +120,7 @@ if __name__ == "__main__":
output = output + '"' + tag + '",'
output = output.rstrip(',')
oFile.write(output + "\n")
complete_report.append(output)
for serie, hashSample in hashGcs.items():
print("Serie: {}".format(serie))
for sample, hashTag in sorted(hashSample.items()):
......@@ -135,6 +137,7 @@ if __name__ == "__main__":
output = output + '"' + tag + '",'
output = output.rstrip(',')
oFile.write(output + "\n")
complete_report.append(output)
# 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))
# for tag, listContent in sorted(hashTag.items()):
# print("\t\tTag: {}".format(tag))
......@@ -144,6 +147,10 @@ if __name__ == "__main__":
# oFile.write("Serie: {}\tSample: {}\tTag: {}\tContent: {}\n".format(serie, sample, tag, content))
saved_files+=1
with open(os.path.join(options.outputPath, f.replace(".xml", ".complete-report.csv")), "w") as oFile:
for line in complete_report:
oFile.write(line + "\n")
print("Processed files: {}".format(processed_files))
print("Saved files: {}".format(saved_files))
......