Transcriptomics

Dataset Information

4

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. 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.

ORGANISM(S): Shewanella oneidensis MR-1  

SUBMITTER: Adam P Arkin   Adam M Deutschbauer  Wenjun Shao  Morgan N Price 

PROVIDER: E-GEOD-58292 | ArrayExpress | 2014-06-12

SECONDARY ACCESSION(S): GSE58292SRP043014PRJNA251904

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

Source:
Action DRS
E-GEOD-58292.idf.txt Idf
E-GEOD-58292.processed.1.zip Processed
E-GEOD-58292.sdrf.txt Txt
Items per page:
1 - 3 of 3

Similar Datasets

2012-07-18 | E-GEOD-39474 | ArrayExpress
2012-07-18 | E-GEOD-39462 | ArrayExpress
2012-04-30 | E-GEOD-25821 | ArrayExpress
2012-10-02 | E-GEOD-39705 | ArrayExpress
2016-12-08 | PXD004090 | Pride
2014-01-01 | S-EPMC4161247 | BioStudies
2015-07-01 | E-GEOD-67564 | ArrayExpress
2013-03-21 | E-GEOD-45313 | ArrayExpress
| PRJNA251904 | ENA
2014-01-01 | S-EPMC3963941 | BioStudies