SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Demultiplexing PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Fastq quality trimming using FastX and a cut-off value of 20 PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Fastq to fasta conversion using FastX PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Size filtering: discarding reads shorter than 12 nt (TRAPL) PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Read mapping using segemehl version 0.13 (TRAPL) PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Coverage calculation and normalisation (TRAPL) PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: wiggle PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Hot phenol (Sharma et al. 2010, Bloomberg 1990, EMBO J) PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5[linebreak]-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5[linebreak]-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	source_name	Escherichia coli MG1655 cells PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	Samples were mixed, incubated on ice for 10 min after which cells were collected by centrifugation at 4150 rpm at 4˚C for 10 min.  Cell pellets were snap frozen in an ethanol/dry ice slurry and stored at -80°C until total RNA could be extracted. PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	medium: M63 PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	source_name	Escherichia coli MG1655 cells PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	Samples were mixed, incubated on ice for 10 min after which cells were collected by centrifugation at 4150 rpm at 4˚C for 10 min.  Cell pellets were snap frozen in an ethanol/dry ice slurry and stored at -80°C until total RNA could be extracted. PGCGROWTHCONDITIONS
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	PMID_25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	contact_name	Konrad,U.,Förstner PGCGROWTHCONDITIONS