Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification and validation of antisense RNAs in Escherichia coli

ABSTRACT: In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions 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 5M-bM-^@M-^Y terminator exonuclease (+TEX samples), which degrades RNAs containing a 5M-bM-^@M-^Y-mono-phosphate (5M-bM-^@M-^Y-P) and, thus, enriching enriches for primary transcripts containing 5M-bM-^@M-^Y-tri-phosphates (5M-bM-^@M-^Y-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5M-bM-^@M-^Y-PPP) and processed RNAs (5M-bM-^@M-^Y-P).

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Konrad FM-CM-6rstner

PROVIDER: E-GEOD-55199 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.

Thomason Maureen K MK Bischler Thorsten T Eisenbart Sara K SK Förstner Konrad U KU Zhang Aixia A Herbig Alexander A Nieselt Kay K Sharma Cynthia M CM Storz Gisela G

Journal of bacteriology 20140929 1

While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions ex ...[more]

PMID: 25266388

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Dataset Information

Identification and validation of antisense RNAs in Escherichia coli

Publications

Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.

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