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Series GSE55199 Query DataSets for GSE55199
Status Public on Oct 18, 2014
Title Identification and validation of antisense RNAs in Escherichia coli
Organism Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by high throughput sequencing
Summary In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions
Overall design To detect the complement of transcripts expressed from E. coli, we collected two independent biological replicates (B1 and B2 samples) from MG1655 wild type strain grown to exponential (OD 600 ~0.4) or stationary phase (OD 600 ~2.0) in LB medium (samples LB 0.4 and LB 2.0, respectively) as well as grown to exponential phase (OD 600 ~0.4) in M63 minimal glucose medium (sample M63 0.4). For all six samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5’ terminator exonuclease (+TEX samples), which degrades RNAs containing a 5’-mono-phosphate (5’-P) and, thus, enriching enriches for primary transcripts containing 5’-tri-phosphates (5’-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5’-PPP) and processed RNAs (5’-P).
Contributor(s) Bischler T, Thomason M, Eisenbart S, Zhang A, Förstner KU, Herbig A, Nieselt K, Sharma CM, Storz G
Citation(s) 25266388
Submission date Feb 20, 2014
Last update date May 15, 2019
Contact name Konrad U. Förstner
Organization name ZB MED - Information Centre for Life Sciences
Department Information Services
Lab Förstner Lab
Street address Gleueler Str. 60
City Cologne
State/province North Rhine-Westphalia
ZIP/Postal code 50931
Country Germany
Platforms (2)
GPL15010 Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)
GPL17024 Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)
Samples (22)
GSM1331409 LB 0.4 B1 TEX neg L1 GA
GSM1331410 LB 0.4 B1 TEX pos L1 GA
GSM1331411 LB 0.4 B2 TEX neg L1 HS1
BioProject PRJNA238884
SRA SRP038698

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Supplementary file Size Download File type/resource
GSE55199_RAW.tar 348.8 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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