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DRNA-seq of Shewanella oneidensis MR-1

ABSTRACT: We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS.

ORGANISM(S): Shewanella oneidensis MR-1

PROVIDER: GSE58292 | GEO | 2014/06/12

SECONDARY ACCESSION(S): PRJNA251904

REPOSITORIES: GEO

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dRNA-seq of Shewanella oneidensis MR-1

Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS. S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.

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Project description:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain. Transcript levels of a WT and hnoC deletion strain were measured after 15 hrs growth, 4 independent replicates were performed for each strain

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