"reference genome: U00096.2"	"characteristics_ch1.1"
"genotype: F-, lambda-, rph-1"	"characteristics_ch1.2"
"strain: K-12"	"characteristics_ch1.3"
"Using a combination of python (3.2.1) and bowtie(0.12.7), from the raw sequencing data, we isolated reads which contained barcode sequences that corresponded to our original list of single molecule barcodes in both forward and reverse reads for each sequence pair that had at most one mismatch. We then aligned the first 28 bases (26 bases for the second sequencing run) of the targeted sequence of both the forward and reverse reads of each cluster to the E. coli genome and kept the sequences that uniquely align fewer than three mismatches and where the two reads did not map to the same sense or antisense strand of the genome.  We used a detailed filtering process to determine the identity of closely-mapped reads. Mapped sequence fragments with a length of at least 1,000 bases were discarded.  All sequences within the same transcription unit that had the same unique tag were analyzed further. We determined that more than one sequence with the same unique tag were identical if the distance between their center positions was less than four base-pairs and if the difference in length was less than 9 base-pairs. Then for each unique sequence, we counted the number of unique barcode tags that appeared to determine the copy number of each sequence and mapped each of them to genes. We include indexed genome viewer files (.sam and .sai) for both experiments using both the conventional method and the digital method."	"data_processing.1"
"Genome build: E. coli [K-12 MG1655 strain (U00096.2)"	"data_processing.2"
"Standard Paired-End Illumina Library Construction Protocol was used with modified adapters containing optimized 20 bp barcode sequences (see original paper).  Samples with barcoded adapters were sequenced on an Illumina HiSeq 2000 with a 2x101 (for the first sequencing run) and 2x51 (for the second) base paired-end reads in one lane."	"extract_protocol_ch1.1"
"E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"RNA from Escherichia coli"	"source_name_ch1.1"
"E_coli_transcriptome_2"	"title.1"
"RNA was purified by a standard protocol using Phenol Chloroform.  Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Epicentre, Illumina).  Then, the conventional Illumina protocol for mRNA Sequencing Sample Preparation was applied with a few modifications (see original paper)."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"reference genome: U00096.2"	"characteristics_ch1.1"
"genotype: F-, lambda-, rph-1"	"characteristics_ch1.2"
"strain: K-12"	"characteristics_ch1.3"
"E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"RNA from Escherichia coli"	"source_name_ch1.1"
"RNA was purified by a standard protocol using Phenol Chloroform.  Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Epicentre, Illumina).  Then, the conventional Illumina protocol for mRNA Sequencing Sample Preparation was applied with a few modifications (see original paper)."	"treatment_protocol_ch1.1"