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

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Kevin Meza Landeros
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1 Agit Air Anti Gtype Gversion Med Name OD Orgn Phase Strain Substrain Supp Technique Temp Vess 1 Agit Air Anti Gtype Gversion Med Name OD Orgn Phase Strain Substrain Supp Technique Temp Vess
2 -gyratory water bath shaking at 240 rpm aerobically (25% O2, 70% N2 and 5% CO2) 9E10 Myc tag fur-8myc NC_000913 LB Wild type control (10 min) OD600 of about 0.3 Escherichia coli mid-log phase K-12 MG1655star 100ug/L adenine RNA-Seq 30 °C (see control sample) flask 2 +gyratory water bath shaking at 240 rpm aerobically (25% O2, 70% N2 and 5% CO2) 9E10 Myc tag fur-8myc NC_000913.2 M63 minimal glucose Fur IP ChIP-Seq Anaerobic A OD600 of ~0.3-0.35 Escherichia coli str. K-12 substr. MG1655 exponential K-12 MG1655 20 min RNA-Seq 30 °C (see control sample) flask
3 - anerobically (95% N2, 5% CO2) Affinity Purified FNR antibody dFNR NC_000913 M9 minimal complete media NsrR_Flagtag_rep3 O.D.600nm 0.3 Escherichia coli str. K-12 substr. MG1655star mid-log phase K-12 MG1655 150 mg/mL ChIP-exo 37 °C 3 + anerobically (95% N2, 5% CO2) Affinity Purified FNR antibody delta_cra U00096.2 M63 σ32 30°C rep1 O.D.600nm 0.3 K-12 MG1655 mid-log phase MG1655star 100ug/L adenine ChIP-Seq 37 °C
4 - Aerobic SeqA ∆fnr U00096.2 glucose (2 g/L) minimal M9 medium NsrR_Flagtag_rep2 OD600 of 0.35 E. coli 16 µM IPTG and 300 µL Cm20 30 degrees C 4 + Aerobic anti-Fur polyclonal antibody ∆fnr ASM584v2 LB Fur IP ChIP-Seq Anaerobic C OD600 of 2.0 Escherichia coli mid-log Fe and rifampicin ChIP-exo 30 degrees C
5 - aerobically Pre-cleared IHF polyclonal antibody dFNR (PK4854) M9 minimal media NsrR_Flagtag_rep1 OD600 of 0.3 Escherichia coli Fe and rifampicin 30 °C 5 + aerobically affinity purified anti-Fur antibody dFNR (PK4854) NC_000913 M9 minimal complete media Fur IP ChIP-Seq Anaerobic B OD600 ≈ 0.5 Escherichia coli K-12 mid-log phase Fe 30 °C
6 - anaerobic RNA polymerase subunit β Fur-8-myc L broth EC18n178 RpoH 2.5 min Time course 1 OD600 of about 0.15 Escherichia coli str. K-12 substr. MG1655 2g/L glutamine 37°C 6 + anaerobic SeqA oxyR-8myc NC_000913 glucose (2 g/L) minimal M9 medium LB 0.4 B2 TEX pos L1 HS2 OD600 of 0.35 MG1655 mid-log pahse Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) 37°C
7 - anaerobically (95% N2 and 5% CO2) Pre-cleared FNR antibody WT MOPS Ecoli_wild-type_rep2_anaerobic 4 µM IPTG 43 °C 7 + anaerobically (95% N2 and 5% CO2) anti-RpoS WT ChIP-Seq M9 minimal media LB 0.4 B2 TEX pos L1 HS1 OD600 of 0.3 Escherichia coli str. K-12 substr. MG1655star stationary acetate 43 °C
8 - anaerobically RNA Polymerase ß monoclonal antibody Wild-Type glucose (2 g/L) minimal W2 medium HNS - Aerobic A 16 µM IPTG 43 °C (see heat sample) 8 + anaerobically Pre-cleared IHF polyclonal antibody wild type LB media Wild type control (10 min) OD600 of about 0.3 150 mg/mL 43 °C (see heat sample)
9 - Anaerobic Pre-cleared H-NS polyclonal antibody TrpR-8myc M9 minimal media HNS - Aerobic B 8 µM IPTG and 300 µL Cm20 37°C 9 + aerobically (70% N2, 25% O2, and 5% CO2) anti-myc Wild-Type L broth LB 0.4 B1 TEX pos L1 GA OD600 of ~0.4 16 µM IPTG and 300 µL Cm20 37°C
10 - σ32 PhtpG::lacZ delta lacX74/ptrc99A (control vector) M9 minimal medium ∆fnr - Anaeroibc 1g/L arginine 10 + Anaerobic anti-RpoB Wildtype M9 medium σ32 30°C rep2 OD600 of about 0.15 DPD
11 - wildtype Ecoli_dFNR_rep1_anaerobic Fe 11 + Pre-cleared FNR antibody lacking the transcription factor Fur and the small RNA RyhB MOPS ChIP-exo GadX pH5.5 2 2g/L glutamine
12 - PK4854 Ptac::fnr - A - 8 µM IPTG nitrate 12 + σ32 gadX-8myc glucose (2 g/L) minimal W2 medium ChIP-exo GadX pH5.5 1 absence of 1 g/L arginine
13 - Flag-tag SeqA old deltaSeqA DPD and rifampicin 13 + RNA polymerase subunit β lacking the transcription factor Fur M9 minimal medium NsrR_Flagtag_rep3 2 g/L glucose
14 - PK8263 SeqA old rep1 glucose 14 + none crp Knock-out strain MOPS minimal glucose media NsrR_Flagtag_rep2 4 µM IPTG
15 - PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH) SeqA old rep2 20 mg/L tryptophan 15 + RNA Polymerase ß monoclonal antibody TrpR-8myc NsrR_Flagtag_rep1 16 µM IPTG
16 - PurR-8myc σ32 ChIP DNA, heat 0.1mM of FeCl2 16 + anti-FLAG mAb PhtpG::lacZ delta lacX74/ptrc99A (control vector) RpoB WT 2 8 µM IPTG and 300 µL Cm20
17 - ΔseqA PurR_glucose_2 4 µM IPTG and 300 µL Cm20 17 + Pre-cleared H-NS polyclonal antibody cra-8myc-tagged RpoB WT 1 1g/L arginine
18 - Fur-8-myc PurR_glucose_1 Adenine 18 + anti-rpoB dFNR Ecoli_wild-type_rep2_anaerobic 0.2% fructose
19 - Δfur SeqA new rep2 0.2% glucose 19 + gadW-8myc HNS - Aerobic A 0.3 M of NaCl
20 - Lrp-8myc SeqA new rep1 rifampicin 20 + wildtype HNS - Aerobic B 0.2% acetate
21 - NsrR EC18n185 RpoH 10 min Time course 3 8 µM IPTG 21 + PK4854 ∆fnr - Anaeroibc 0.2%
22 - ∆hns/∆stpA σ32 43°C rep2 0.2mM of DPD 22 + {delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12 TrpR_glucose DPD and rifampicin
23 - ArgR-8myc σ32 43°C rep1 DPD 23 + gadE-8myc WT_ChIPSeq_2 1 µM FeSO4
24 - EC18n169 RpoH 5 min Time course 2 iron 24 + Combined input ChIP-exo GadE pH5.5 2 20 mg/L tryptophan
25 - HNS - Anaerobic A 10 mM leucine 25 + delta-gadE ChIP-exo GadE pH5.5 1 250 uM of paraquat
26 + ompR-8myc WT_ChIPSeq_1 0.1mM of FeCl2
27 + lacking the small RNA RyhB WT PQ 2 Adenine
28 + Flag-tag ChIP-exo GadW pH5.5 1 rifampicin dissolved in methanol
29 + {delta}tonB, {delta}feoA, {delta}zupT K12 OmpR NaCl 2 nitrate
30 + PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH) OmpR NaCl 1 0.2% glucose
31 + delta-gadX ChIP-exo GadW pH5.5 2 fructose
32 + delta-gadW Ptac::fnr - A - 8 µM IPTG 10 µM FeSO4
33 + PurR-8myc SeqA old deltaSeqA 8 µM IPTG
34 + delta-oxyR ΔgadW pH5.5 1 0.2mM of DPD
35 + soxR-8myc ΔoxyR PQ 1 2 hours
36 + ΔseqA ΔoxyR PQ 2 30 min
37 + PK8263 ΔgadW pH5.5 2 4 µM IPTG and 300 µL Cm20
38 + delta-soxS ∆ryhB Aerobic presence or absence of 1 g/L arginine
39 + delta-soxR σ32 ChIP DNA, heat 1mM IPTG
40 + ∆hns/∆stpA Δfur with Fe 2 (RNA-seq) glucose
41 + soxS-8myc RpoH induced (20 min) 2h
42 + Wild-type SoxR PQ 1 10 mM leucine
43 + Δfur SoxR PQ 2
44 + Lrp-8myc LB 2.0 B2 TEX neg L1 HS1
45 + ArgR-8myc PurR_glucose_2
46 + NsrR PurR_glucose_1
47 + cra Knock-out strain LB 2.0 B2 TEX neg L1 HS2
48 + ompR deletion mutant SeqA new rep2
49 + WT with Fe 2 (RNA-seq)
50 + RpoH induced (2.5 min)
51 + Δcra acetate 1
52 + Δcra acetate 2
53 + Nac_ChIPSeq
54 + EC18n185 RpoH 10 min Time course 3
55 + σ32 43°C rep2
56 + RpoB with Fe 1 (ChIP-exo)
57 + CsiR_RNASeq
58 + ΔsoxR PQ 1
59 + EC18n169 RpoH 5 min Time course 2
60 + CsiR_ChIPSeq
61 + HNS - Anaerobic A
62 + Fur IP ChIP-Seq Aerobic A
63 + Fur IP ChIP-Seq Aerobic B
26 HNS - Anaerobic B 64 HNS - Anaerobic B
65 + σ32 43°C rep1
66 + LB 2.0 B1 TEX pos L2 HS2
67 + OxyR PQ 2
27 Wild type control (0 min) 68 Wild type control (0 min)
28 - Ptac::fnr - B - 4 µM IPTG 69 + WT acetate 1
29 - RpoH induced (2.5 min) 70 + WT acetate 2
71 + M63 0.4 B2 TEX pos L1 HS1
72 + M63 0.4 B2 TEX pos L1 HS2
73 + SeqA new rep1
74 + SeqA old rep2
30 IHF - Anaerobic B 75 IHF - Anaerobic B
31 IHF - Anaerobic A 76 IHF - Anaerobic A
32 RNAP old rep2 77 RNAP old rep2
33 RpoH induced (0 min) 78 RpoH induced (0 min)
34 - RNAP old rep1 79 + EC18n180 RpoH 10 min Time course 1
35 EC18n122 RpoH 10 min Time course 4 80 EC18n122 RpoH 10 min Time course 4
81 + LB 2.0 B2 TEX pos L1 HS1
36 Crosslink 82 Crosslink
37 - RpoH induced (20 min) 83 + LB 2.0 B2 TEX pos L1 HS2
84 + Cra glucose 1
85 + Cra glucose 2
86 + Cra fructose 1
87 + Cra fructose 2
88 + Wild-type Aerobic A
89 + Wild-type Aerobic B
90 + RpoB with DPD and rifampicin 1 (ChIP-exo)
91 + SoxS PQ 2
92 + SoxS PQ 1
93 + EC18n178 RpoH 2.5 min Time course 1
38 Wild type control (20 min) 94 Wild type control (20 min)
95 + pT7_ChIPSeq_1
96 + pT7_ChIPSeq_2
39 EC18n182 RpoH 0 min Time course 3 97 EC18n182 RpoH 0 min Time course 3
98 + RNAP old rep1
40 Lrp_Leu_1 99 Lrp_Leu_1
41 Lrp_Leu_3 100 Lrp_Leu_3
42 Lrp_Leu_2 101 Lrp_Leu_2
102 + RpoB with DPD 1 (ChIP-exo)
103 + Cra acetate 1
104 + Cra acetate 2
43 EC18n171 RpoH 20 min Time course 2 105 EC18n171 RpoH 20 min Time course 2
106 + EC18n179 RpoH 5 min Time course 1
44 Ptac::fnr - A - 16 µM IPTG 107 Ptac::fnr - A - 16 µM IPTG
108 + ∆fur ∆ryhB Aerobic B
109 + Nac_RNASeq
110 + LB 2.0 B1 TEX pos L1 GA
111 + ∆fur Anaerobic A
45 σ32 30°C short RNase 112 σ32 30°C short RNase
46 EC18n181 RpoH 20 min Time course 1 113 EC18n181 RpoH 20 min Time course 1
47 - PurR_Adenine_2 114 + M63 0.4 B2 TEX neg L1 HS1
48 - PurR_Adenine_1 115 + M63 0.4 B2 TEX neg L1 HS2
49 EC18n168 RpoH 2.5 min Time course 2 116 EC18n168 RpoH 2.5 min Time course 2
117 + Δcra glucose 1
118 + Δcra glucose 2
50 Lrp_NH4Cl_2 119 Lrp_NH4Cl_2
51 Lrp_NH4Cl_3 120 Lrp_NH4Cl_3
52 Lrp_NH4Cl_1 121 Lrp_NH4Cl_1
53 - σ32 30°C rep1 122 + LB 2.0 B1 TEX neg L2 HS2
54 - σ32 30°C rep2 123 + ΔsoxS PQ 1
124 + Δcra fructose 1
125 + Δcra fructose 2
126 + WT_RNASeq
127 + WT glucose 1
128 + WT glucose 2
129 + Wild type control (5 min)
55 EC18n184 RpoH 5 min Time course 3 130 EC18n184 RpoH 5 min Time course 3
131 + Fur IP ChIP-Seq Aerobic C
132 + RpoB with Fe and rifampicin 1 (ChIP-exo)
133 + Fur with Fe 2 (ChIP-exo)
56 FNR - Anaerobic - A 134 FNR - Anaerobic - A
135 + WT with Fe 1 (RNA-seq)
57 FNR - Anaerobic - C 136 FNR - Anaerobic - C
58 FNR - Anaerobic - B 137 FNR - Anaerobic - B
138 + ΔompR NaCl 2
139 + ΔompR NaCl 1
140 + Ecoli_dFNR_rep1_anaerobic
59 Ptac::fnr - A - 4 µM IPTG 141 Ptac::fnr - A - 4 µM IPTG
142 + LB 2.0 B2 TEX neg L2 HS2
143 + PurR_Adenine_1
60 Ecoli_wild-type_rep1_anaerobic 144 Ecoli_wild-type_rep1_anaerobic
61 EC18n167 RpoH 0 min Time course 2 145 EC18n167 RpoH 0 min Time course 2
146 + Wild-type Anaerobic B
147 + Fur with Fe 1 (ChIP-exo)
62 FNR - ∆hns∆stpA A 148 FNR - ∆hns∆stpA A
149 + RpoB with Fe 2 (ChIP-exo)
63 FNR - ∆hns∆stpA B 150 FNR - ∆hns∆stpA B
151 + RpoB ∆cra 2
152 + RpoB with DPD and rifampicin 2 (ChIP-exo)
153 + RpoB ∆cra 1
154 + WT NaCl 1
155 + WT NaCl 2
156 + WT with DPD 1 (RNA-seq)
157 + LB 0.4 B1 TEX neg L1 GA
64 Ptac::fnr - B - 8 µM IPTG 158 Ptac::fnr - B - 8 µM IPTG
65 ArgR_Arginine_2 159 ArgR_Arginine_2
66 - TrpR_glucose 160 + LB 0.4 B2 TEX neg L1 HS2
161 + LB 0.4 B2 TEX neg L1 HS1
67 ArgR_Arginine_1 162 ArgR_Arginine_1
68 - Escherichia coli str. K-12 substr. MG1655
69 ArgR_NH4Cl_1 163 ArgR_NH4Cl_1
70 - ArgR_NH4Cl_2 164 + Escherichia coli str. K-12 substr. MG1655
165 + OxyR PQ 1
166 + ΔgadX pH5.5 2
167 + ∆fur ∆ryhB Anaerobic A
168 + ΔgadX pH5.5 1
169 + Fur IP ChIP-Seq Anaerobic, Iron Deficient B
170 + Δfur with Fe 1 (RNA-seq)
171 + Fur IP ChIP-Seq Anaerobic, Iron Deficient A
71 ß - Anaerobic - A 172 ß - Anaerobic - A
72 ß - Anaerobic - B 173 ß - Anaerobic - B
73 σ32 ChIP DNA, control 174 σ32 ChIP DNA, control
74 SeqA new deltaSeqA 175 SeqA new deltaSeqA
75 - EC18n177 RpoH 0 min Time course 1 176 + M63 0.4 B1 TEX neg L1 GA
76 TrpR_Trp 177 TrpR_Trp
77 Ptac::fnr - B - 16 µM IPTG 178 Ptac::fnr - B - 16 µM IPTG
78 ß - Aerobic - A 179 ß - Aerobic - A
180 + Ptac::fnr - B - 4 µM IPTG
79 ß - Aerobic - B 181 ß - Aerobic - B
182 + EC18n177 RpoH 0 min Time course 1
80 σ32 43°C short RNase 183 σ32 43°C short RNase
184 + ∆ryhB Anaerobic
185 + Input ChIP-Seq
186 + Δfur with DPD 1 (RNA-seq)
81 RpoH induced (5 min) 187 RpoH induced (5 min)
188 + ∆fur Anaerobic B
82 FNR - Anaerobic - Affinity Purified - B 189 FNR - Anaerobic - Affinity Purified - B
83 EC18n186 RpoH 20 min Time course 3 190 EC18n186 RpoH 20 min Time course 3
84 FNR - Anaerobic - Affinity Purified - A 191 FNR - Anaerobic - Affinity Purified - A
192 + ChIP-exo RpoS pH5.5 2
193 + RpoB with DPD 2 (ChIP-exo)
194 + ChIP-exo RpoS pH5.5 1
195 + ΔsoxR PQ 2
196 + PurR_Adenine_2
85 Ptac::fnr - C - 16 µM IPTG 197 Ptac::fnr - C - 16 µM IPTG
198 + WT PQ 1
86 EC18n170 RpoH 10 min Time course 2 199 EC18n170 RpoH 10 min Time course 2
200 + ∆fur ∆ryhB Anaerobic B
201 + M63 0.4 B1 TEX pos L1 GA
87 RpoH induced (10 min) 202 RpoH induced (10 min)
203 + Wild-type Anaerobic A
204 + ArgR_NH4Cl_2
205 + LB 2.0 B1 TEX neg L1 GA
206 + WT with DPD 2 (RNA-seq)
207 + ∆fur Anaerobic [IP vs nput]
88 EC18n183 RpoH 2.5 min Time course 3 208 EC18n183 RpoH 2.5 min Time course 3
89 - EC18n180 RpoH 10 min Time course 1 209 + ∆fur ∆ryhB Aerobic A
90 - EC18n179 RpoH 5 min Time course 1 210 + RpoB ∆crp 2
91 - Wild type control (5 min) 211 + NtrC_ChIPSeq
212 + RpoB ∆crp 1
213 + WT fructose 1
214 + ΔgadE pH5.5 2
215 + ΔgadE pH5.5 1
216 + WT fructose 2
217 + OmpR_ChIPSeq
218 + RpoB with Fe and rifampicin 2 (ChIP-exo)
219 + WT pH5.5 1
220 + WT pH5.5 2
92 Wild type control (2.5 min) 221 Wild type control (2.5 min)
93 Ecoli_dFNR_rep2_anaerobic 222 Ecoli_dFNR_rep2_anaerobic
223 + Fur with DPD 1 (ChIP-exo)
224 + ∆fur Aerobic A
225 + ∆fur Aerobic B
226 + ΔsoxS PQ 2
227 + Δfur with DPD 2 (RNA-seq)
228 + Fur with DPD 2 (ChIP-exo)
229 + SeqA old rep1
230 + LB 2.0 B2 TEX pos L2 HS2
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