Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcript structures in Shewanella oneidensis MR-1

ABSTRACT: 5' RNA-Seq of mRNA from S. oneidensis MR-1 grown aerobically in defined lactate medium One lane of sequence for a 5' RNASeq library from RNA treated with exonuclease to remove degraded transcripts, with single-end 40-nt reads

ORGANISM(S): Shewanella oneidensis MR-1

SUBMITTER: Morgan Price

PROVIDER: E-GEOD-39474 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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.

2014-06-12 | E-GEOD-58292 | biostudies-arrayexpress

Transcript structures in Shewanella oneidensis MR-1

Project description:5' RNASeq of mRNA from S. oneidensis MR-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45313 | biostudies-arrayexpress

Conservation of transcription start sites within genes across a bacterial genus

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-06-09 | E-GEOD-58337 | biostudies-arrayexpress

Transcript structures in Shewanella amazonensis SB2B

Project description:5' RNASeq of mRNA from Shewanella amazonensis SB2B grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45317 | biostudies-arrayexpress

Transcript structures in Shewanella sp W3-18-1

Project description:5' RNASeq of mRNA from Shewanella sp W3-18-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45318 | biostudies-arrayexpress

Transcript structures in Shewanella putrefaciens CN-32

Project description:5' RNASeq of mRNA from Shewanella putrefaciens CN-32 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45312 | biostudies-arrayexpress

Transcript structures in Shewanella sp ANA-3

Project description:5' RNASeq of mRNA from Shewanella sp ANA-3 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45311 | biostudies-arrayexpress

Transcript structures in Shewanella sp MR-7

Project description:5' RNASeq of mRNA from Shewanella sp MR-7 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45315 | biostudies-arrayexpress

Transcript structures in Shewanella sp MR-4

Project description:5' RNASeq of mRNA from Shewanella sp MR-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45314 | biostudies-arrayexpress

Transcript structures in Shewanella loihica PV-4

Project description:5' RNASeq of mRNA from Shewanella loihica PV-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

2013-03-21 | E-GEOD-45316 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data