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

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Kevin Meza Landeros
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Agit Air Anti Gtype Gversion Med Name OD Orgn Phase Strain Substrain Supp Technique Temp Vess
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
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
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
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
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
anaerobically (95% N2 and 5% CO2) Pre-cleared FNR antibody WT MOPS Ecoli_wild-type_rep2_anaerobic 4 µM IPTG 43 °C
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)
Anaerobic Pre-cleared H-NS polyclonal antibody TrpR-8myc M9 minimal media HNS - Aerobic B 8 µM IPTG and 300 µL Cm20 37°C
σ32 PhtpG::lacZ delta lacX74/ptrc99A (control vector) M9 minimal medium ∆fnr - Anaeroibc 1g/L arginine
wildtype Ecoli_dFNR_rep1_anaerobic Fe
PK4854 Ptac::fnr - A - 8 µM IPTG nitrate
Flag-tag SeqA old deltaSeqA DPD and rifampicin
PK8263 SeqA old rep1 glucose
PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH) SeqA old rep2 20 mg/L tryptophan
PurR-8myc σ32 ChIP DNA, heat 0.1mM of FeCl2
ΔseqA PurR_glucose_2 4 µM IPTG and 300 µL Cm20
Fur-8-myc PurR_glucose_1 Adenine
Δfur SeqA new rep2 0.2% glucose
Lrp-8myc SeqA new rep1 rifampicin
NsrR EC18n185 RpoH 10 min Time course 3 8 µM IPTG
∆hns/∆stpA σ32 43°C rep2 0.2mM of DPD
ArgR-8myc σ32 43°C rep1 DPD
EC18n169 RpoH 5 min Time course 2 iron
HNS - Anaerobic A 10 mM leucine
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
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
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
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
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
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
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)
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
Anaerobic anti-RpoB Wildtype M9 medium σ32 30°C rep2 OD600 of about 0.15 DPD
Pre-cleared FNR antibody lacking the transcription factor Fur and the small RNA RyhB MOPS ChIP-exo GadX pH5.5 2 2g/L glutamine
σ32 gadX-8myc glucose (2 g/L) minimal W2 medium ChIP-exo GadX pH5.5 1 absence of 1 g/L arginine
RNA polymerase subunit β lacking the transcription factor Fur M9 minimal medium NsrR_Flagtag_rep3 2 g/L glucose
none crp Knock-out strain MOPS minimal glucose media NsrR_Flagtag_rep2 4 µM IPTG
RNA Polymerase ß monoclonal antibody TrpR-8myc NsrR_Flagtag_rep1 16 µM IPTG
anti-FLAG mAb PhtpG::lacZ delta lacX74/ptrc99A (control vector) RpoB WT 2 8 µM IPTG and 300 µL Cm20
Pre-cleared H-NS polyclonal antibody cra-8myc-tagged RpoB WT 1 1g/L arginine
anti-rpoB dFNR Ecoli_wild-type_rep2_anaerobic 0.2% fructose
gadW-8myc HNS - Aerobic A 0.3 M of NaCl
wildtype HNS - Aerobic B 0.2% acetate
PK4854 ∆fnr - Anaeroibc 0.2%
{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12 TrpR_glucose DPD and rifampicin
gadE-8myc WT_ChIPSeq_2 1 µM FeSO4
Combined input ChIP-exo GadE pH5.5 2 20 mg/L tryptophan
delta-gadE ChIP-exo GadE pH5.5 1 250 uM of paraquat
ompR-8myc WT_ChIPSeq_1 0.1mM of FeCl2
lacking the small RNA RyhB WT PQ 2 Adenine
Flag-tag ChIP-exo GadW pH5.5 1 rifampicin dissolved in methanol
{delta}tonB, {delta}feoA, {delta}zupT K12 OmpR NaCl 2 nitrate
PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH) OmpR NaCl 1 0.2% glucose
delta-gadX ChIP-exo GadW pH5.5 2 fructose
delta-gadW Ptac::fnr - A - 8 µM IPTG 10 µM FeSO4
PurR-8myc SeqA old deltaSeqA 8 µM IPTG
delta-oxyR ΔgadW pH5.5 1 0.2mM of DPD
soxR-8myc ΔoxyR PQ 1 2 hours
ΔseqA ΔoxyR PQ 2 30 min
PK8263 ΔgadW pH5.5 2 4 µM IPTG and 300 µL Cm20
delta-soxS ∆ryhB Aerobic presence or absence of 1 g/L arginine
delta-soxR σ32 ChIP DNA, heat 1mM IPTG
∆hns/∆stpA Δfur with Fe 2 (RNA-seq) glucose
soxS-8myc RpoH induced (20 min) 2h
Wild-type SoxR PQ 1 10 mM leucine
Δfur SoxR PQ 2
Lrp-8myc LB 2.0 B2 TEX neg L1 HS1
ArgR-8myc PurR_glucose_2
NsrR PurR_glucose_1
cra Knock-out strain LB 2.0 B2 TEX neg L1 HS2
ompR deletion mutant SeqA new rep2
WT with Fe 2 (RNA-seq)
RpoH induced (2.5 min)
Δcra acetate 1
Δcra acetate 2
Nac_ChIPSeq
EC18n185 RpoH 10 min Time course 3
σ32 43°C rep2
RpoB with Fe 1 (ChIP-exo)
CsiR_RNASeq
ΔsoxR PQ 1
EC18n169 RpoH 5 min Time course 2
CsiR_ChIPSeq
HNS - Anaerobic A
Fur IP ChIP-Seq Aerobic A
Fur IP ChIP-Seq Aerobic B
HNS - Anaerobic B
σ32 43°C rep1
LB 2.0 B1 TEX pos L2 HS2
OxyR PQ 2
Wild type control (0 min)
Ptac::fnr - B - 4 µM IPTG
RpoH induced (2.5 min)
WT acetate 1
WT acetate 2
M63 0.4 B2 TEX pos L1 HS1
M63 0.4 B2 TEX pos L1 HS2
SeqA new rep1
SeqA old rep2
IHF - Anaerobic B
IHF - Anaerobic A
RNAP old rep2
RpoH induced (0 min)
RNAP old rep1
EC18n180 RpoH 10 min Time course 1
EC18n122 RpoH 10 min Time course 4
LB 2.0 B2 TEX pos L1 HS1
Crosslink
RpoH induced (20 min)
LB 2.0 B2 TEX pos L1 HS2
Cra glucose 1
Cra glucose 2
Cra fructose 1
Cra fructose 2
Wild-type Aerobic A
Wild-type Aerobic B
RpoB with DPD and rifampicin 1 (ChIP-exo)
SoxS PQ 2
SoxS PQ 1
EC18n178 RpoH 2.5 min Time course 1
Wild type control (20 min)
pT7_ChIPSeq_1
pT7_ChIPSeq_2
EC18n182 RpoH 0 min Time course 3
RNAP old rep1
Lrp_Leu_1
Lrp_Leu_3
Lrp_Leu_2
RpoB with DPD 1 (ChIP-exo)
Cra acetate 1
Cra acetate 2
EC18n171 RpoH 20 min Time course 2
EC18n179 RpoH 5 min Time course 1
Ptac::fnr - A - 16 µM IPTG
∆fur ∆ryhB Aerobic B
Nac_RNASeq
LB 2.0 B1 TEX pos L1 GA
∆fur Anaerobic A
σ32 30°C short RNase
EC18n181 RpoH 20 min Time course 1
PurR_Adenine_2
PurR_Adenine_1
M63 0.4 B2 TEX neg L1 HS1
M63 0.4 B2 TEX neg L1 HS2
EC18n168 RpoH 2.5 min Time course 2
Δcra glucose 1
Δcra glucose 2
Lrp_NH4Cl_2
Lrp_NH4Cl_3
Lrp_NH4Cl_1
σ32 30°C rep1
σ32 30°C rep2
LB 2.0 B1 TEX neg L2 HS2
ΔsoxS PQ 1
Δcra fructose 1
Δcra fructose 2
WT_RNASeq
WT glucose 1
WT glucose 2
Wild type control (5 min)
EC18n184 RpoH 5 min Time course 3
Fur IP ChIP-Seq Aerobic C
RpoB with Fe and rifampicin 1 (ChIP-exo)
Fur with Fe 2 (ChIP-exo)
FNR - Anaerobic - A
WT with Fe 1 (RNA-seq)
FNR - Anaerobic - C
FNR - Anaerobic - B
ΔompR NaCl 2
ΔompR NaCl 1
Ecoli_dFNR_rep1_anaerobic
Ptac::fnr - A - 4 µM IPTG
LB 2.0 B2 TEX neg L2 HS2
PurR_Adenine_1
Ecoli_wild-type_rep1_anaerobic
EC18n167 RpoH 0 min Time course 2
Wild-type Anaerobic B
Fur with Fe 1 (ChIP-exo)
FNR - ∆hns∆stpA A
RpoB with Fe 2 (ChIP-exo)
FNR - ∆hns∆stpA B
RpoB ∆cra 2
RpoB with DPD and rifampicin 2 (ChIP-exo)
RpoB ∆cra 1
WT NaCl 1
WT NaCl 2
WT with DPD 1 (RNA-seq)
LB 0.4 B1 TEX neg L1 GA
Ptac::fnr - B - 8 µM IPTG
ArgR_Arginine_2
TrpR_glucose
LB 0.4 B2 TEX neg L1 HS2
LB 0.4 B2 TEX neg L1 HS1
ArgR_Arginine_1
Escherichia coli str. K-12 substr. MG1655
ArgR_NH4Cl_1
ArgR_NH4Cl_2
Escherichia coli str. K-12 substr. MG1655
OxyR PQ 1
ΔgadX pH5.5 2
∆fur ∆ryhB Anaerobic A
ΔgadX pH5.5 1
Fur IP ChIP-Seq Anaerobic, Iron Deficient B
Δfur with Fe 1 (RNA-seq)
Fur IP ChIP-Seq Anaerobic, Iron Deficient A
ß - Anaerobic - A
ß - Anaerobic - B
σ32 ChIP DNA, control
SeqA new deltaSeqA
EC18n177 RpoH 0 min Time course 1
M63 0.4 B1 TEX neg L1 GA
TrpR_Trp
Ptac::fnr - B - 16 µM IPTG
ß - Aerobic - A
Ptac::fnr - B - 4 µM IPTG
ß - Aerobic - B
EC18n177 RpoH 0 min Time course 1
σ32 43°C short RNase
∆ryhB Anaerobic
Input ChIP-Seq
Δfur with DPD 1 (RNA-seq)
RpoH induced (5 min)
∆fur Anaerobic B
FNR - Anaerobic - Affinity Purified - B
EC18n186 RpoH 20 min Time course 3
FNR - Anaerobic - Affinity Purified - A
ChIP-exo RpoS pH5.5 2
RpoB with DPD 2 (ChIP-exo)
ChIP-exo RpoS pH5.5 1
ΔsoxR PQ 2
PurR_Adenine_2
Ptac::fnr - C - 16 µM IPTG
WT PQ 1
EC18n170 RpoH 10 min Time course 2
∆fur ∆ryhB Anaerobic B
M63 0.4 B1 TEX pos L1 GA
RpoH induced (10 min)
Wild-type Anaerobic A
ArgR_NH4Cl_2
LB 2.0 B1 TEX neg L1 GA
WT with DPD 2 (RNA-seq)
∆fur Anaerobic [IP vs nput]
EC18n183 RpoH 2.5 min Time course 3
EC18n180 RpoH 10 min Time course 1
EC18n179 RpoH 5 min Time course 1
Wild type control (5 min)
∆fur ∆ryhB Aerobic A
RpoB ∆crp 2
NtrC_ChIPSeq
RpoB ∆crp 1
WT fructose 1
ΔgadE pH5.5 2
ΔgadE pH5.5 1
WT fructose 2
OmpR_ChIPSeq
RpoB with Fe and rifampicin 2 (ChIP-exo)
WT pH5.5 1
WT pH5.5 2
Wild type control (2.5 min)
Ecoli_dFNR_rep2_anaerobic
Fur with DPD 1 (ChIP-exo)
∆fur Aerobic A
∆fur Aerobic B
ΔsoxS PQ 2
Δfur with DPD 2 (RNA-seq)
Fur with DPD 2 (ChIP-exo)
SeqA old rep1
LB 2.0 B2 TEX pos L2 HS2
......