"strain: MG1655"	"characteristics_ch1.1"
"mrna synthesis: in vivo"	"characteristics_ch1.2"
"CASAVA version 1.4"	"data_processing.1"
"A single large fastq  format file of high quality reads (Q ≥ 30) was split into about 10 smaller files by using a shell script splitReads.sh"	"data_processing.2"
"The obtained reads were aligned  and mapped to the pPR9 plasmid DNA sequences using   Bowtie 0.12.7."	"data_processing.3"
"The numbers of 4 bases A, T, G, C, and N were counted in each position of the mapped reads by using the program  SAMtools 0.1.18 with supplemental use of a Perl script."	"data_processing.4"
"Each type of error rates per position was determined as  the number of sequence reads with a particular type of base-substitution  divided by the number of the reads with the reference base in each DNA  position."	"data_processing.5"
"Genome_build: pPR9 plasmid (ref is Kashlec et al., 1989, PMID: 2547695)"	"data_processing.6"
"Supplementary_files_format_and_content: tab-delimited text file of transition error rate per position. The position is corresponding to the position of \"Sequenced region of pPR9 plasmid\" (one of the attached txt file)."	"data_processing.7"
"In vitro RNA preparation: The 5.7 kb RNA was purified from the digested DNA, NTPs, abortive oligo-RNA products, and proteins by Acidic phenol extraction, G50 spin column, followed by EtOH precipitation."	"extract_protocol_ch1.1"
"In vivo RNA preparation: The cells in 200 ml culture were harvested and resuspended with a solution containing 0.5% SDS, 20 mM sodium acetate (pH 5.5), and 10 mM EDTA. The suspended cells were mixed with an equal volume of pre-warmed saturated phenol (20 mM sodium acetate, 10 mM EDTA pH 5.5) and incubated for 5 min at 60  C. The mixture was centrifuged, and RNA and DNA were precipitated with ethanol from the supernatant. The pellet was dissolved in DNase I buffer with 10U of DNaseI and incubated for 30 min. RNA was separated from the digested DNA by acidic phenol extraction followed by G-50 Micro column (GE Healthcare) purification, and then precipitated with ethanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis."	"extract_protocol_ch1.2"
"The cells culture were harvested and resuspended with a  solution containing 0.5% SDS, 20 mM sodium acetate (pH 5.5), and 10 mM  EDTA. The suspended cells were mixed with an equal volume of pre-warmed  saturated phenol (20 mM sodium acetate, 10 mM EDTA pH 5.5) and incubated  for 5 min at 60˚C."	"extract_protocol_ch1.3"
"We established a method for preparing five different cDNA  libraries each with its own barcode for Illumina sequencing. Each 6-nt barcode allows multiplexing all five in vitro and  in vivo preparations in a single sequencing analysis. our method introduces internal control sequences to the library  that are subjected to the artifact errors, but are not for RNAP  errors. The 5’ fragment of the 5.7 kb RNA  transcripts was reverse transcribed to make the cDNA.  The cDNA was subjected to PCR reactions that generated  six  200 bp segments. The primers contained a specific barcode  for each of the five starting preparations and the inner Illuminasequencing  adapters. The 2nd-step of PCR generated  the final cDNA libraries for the Illumina sequencing by using  the 1st-step PCR product as a template and primers containing  the outer sequencing adapters in the 5’ tails."	"extract_protocol_ch1.4"
"mRNA-seq with barcode (Illumina  TruSeq Index 1-5)"	"extract_protocol_ch1.5"
"Cells were cultured in LB medium containing ampicillin at 28˚C. The overnight cell culture was inoculated into the fresh  medium at 1/70 (v/v) and was incubated for  2 hr at 28˚C (OD600 reached  0.35) and then for 2 hr at 42˚C (OD600 reached 2.3) to induce the PR promoter."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E.coli strain MG1655"	"source_name_ch1.1"
"in vivo"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: MG1655"	"characteristics_ch1.1"
"mrna synthesis: in vivo"	"characteristics_ch1.2"
"Cells were cultured in LB medium containing ampicillin at 28˚C. The overnight cell culture was inoculated into the fresh  medium at 1/70 (v/v) and was incubated for  2 hr at 28˚C (OD600 reached  0.35) and then for 2 hr at 42˚C (OD600 reached 2.3) to induce the PR promoter."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E.coli strain MG1655"	"source_name_ch1.1"