SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	source_name	Total RNA from bacterial culture PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	protocol: small RNA DicF PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	source_name	Total RNA from bacterial culture PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
SRR3103790	GSE76916	GSM2040692	GPL15010	PMID_	DicF rep3	Gene expression changes during overexpression of bacterial small RNA, DicF	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Carin,K.,Vanderpool PGCGROWTHCONDITIONS