SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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. PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome build: E. coli [K-12 MG1655 strain (U00096.2) PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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. PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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. PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	source_name	RNA from Escherichia coli PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	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). PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	reference genome: U00096.2 PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: F-, lambda-, rph-1 PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	strain: K-12 PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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. PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	source_name	RNA from Escherichia coli PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	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). PGCGROWTHCONDITIONS
SRR389819	GSE34449	GSM849370	GPL15010	PMID_22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Tony,Z,Jia PGCGROWTHCONDITIONS