"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"	"data_processing.1"
"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"	"data_processing.2"
"Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus)."	"data_processing.3"
"Genome_build: Escherichia coli K12 str MG1655"	"data_processing.4"
"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."	"data_processing.5"
"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."	"extract_protocol_ch1.1"
"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."	"extract_protocol_ch1.2"
"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."	"extract_protocol_ch1.3"
"Escherichia coli"	"organism_ch1.1"
"E. coli cells_HS30min"	"source_name_ch1.1"
"HS30min_r2_HiSeq"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: K12"	"characteristics_ch1.1"
"substrain: MG1655"	"characteristics_ch1.2"
"culture/growth condition: Heatshock 30min"	"characteristics_ch1.3"
"Escherichia coli"	"organism_ch1.1"
"E. coli cells_HS30min"	"source_name_ch1.1"