SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	RNA-seq sequence reads were mapped onto the reference genome (E. coli MG1655 NC_000913.3) using bowtie 1.1.2with the following options “-X 1000 -n 2 −3 3”. PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Read count was performed using summarizeOverlaps from the R GenomicAlignments package, using options “mode=“IntersectionStrict”, singleEnd=FALSE, ignore.strand=FALSE, preprocess.reads=invertStrand” PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: E.coli genome(NC_000913.3) PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Comma-separated text file includes TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	For RNA-seq, 3 mL of culture were mixed with 6 mL of RNAprotect bacteria reagent (Qiagen) and processed according to the manufacturer’s instructions. Cell pellets were frozen and stored at -80 °C until processed. RNA was extracted using the Zymo Research Quick RNA fungal/bacterial microprep kit, according to the manufacturer[linebreak]s instructions. Ribosomal RNA was removed from total RNA preparations using RNase H. First, traces of genomic DNA were removed with a DNase I treatment. Then, secondary structures in the ribosomal RNA were removed by heating to 90 °C for one second. A set of 32-mer DNA oligonucleotide probes complementary to 5S, 16S, and 23S rRNA subunits and spaced nine bases apart were then annealed at 65 °C followed by digestion with Hybridase (Lucigen), a thermostable RNase H.  Hybridase was added at 65 °C, the reaction was incubated for 20 minutes at that temperature, then heated again to 90 °C for one second to remove remaining secondary structures, and finally returned to 65 °C for 10 minutes. The reaction was quickly quenched by the addition of guanidine thiocyanate while still at 65 °C before purifying the mRNA with a Zymo Research RNA Clean and Concentrator kit using their 200 nt cutoff protocol. Carryover oligos were removed with a DNase I digestion which was started at room temperature and gradually increased to 42 °C over a half hour. This was followed up with another column purification as stated above. PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Paired-end library preparation was done using the KAPA RNA HyperPrep kit following the manufacturer’s instructions. PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	source_name	bacterial cells PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	media: LB medium PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: {delta}cpxR PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	source_name	bacterial cells PGCGROWTHCONDITIONS
SRR10907649	GSE143855	GSM4275451	GPL24659	PMID_33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Bernhard,O.,Palsson PGCGROWTHCONDITIONS