SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	strain: K-12 PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PGCGROWTHCONDITIONS
SRR5416993	GSE97406	GSM2564001	GPL16085	PMID_	WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	contact_name	Alan,J,Wolfe PGCGROWTHCONDITIONS