SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	E. coli cells_M-P2h PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: K12 PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	substrain: MG1655 PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	E. coli cells_M-P2h PGCGROWTHCONDITIONS
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	PMID_23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Zhengchang,,Su PGCGROWTHCONDITIONS