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Shewanella oneidensis MR-1

ABSTRACT: Shewanella oneidensis Transcriptome

PROVIDER: PRJNA668666 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR12815949_1.fastq.gz	Fastqsanger.gz
	SRR12815949_2.fastq.gz	Fastqsanger.gz
	SRR12815950_1.fastq.gz	Fastqsanger.gz
	SRR12815950_2.fastq.gz	Fastqsanger.gz
	SRR12815951_1.fastq.gz	Fastqsanger.gz

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1 - 5 of 12

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Quantitative proteome of Shewanella oneidensis MR-1

Project description:We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive ammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture.

2016-12-08 | PXD004090 | Pride

Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

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Expression data from Shewanella oneidensis MR-1 in time series experiment

Project description:The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium) To explore the effect of various growth phases in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles growth in two sets media was compared to each other. Strain was grown in chemostat at 20% O2 in batch culture. Samples were collected in duplicate from both experiments.

2012-04-30 | E-GEOD-25821 | biostudies-arrayexpress

dRNA-seq of Shewanella oneidensis MR-1

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Transcriptional targets of Shewanella oneidensis HnoC (SO_2540)

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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.

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

Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1 Expression data for 15 growth conditions in mid-exponential phase and expression data across growth phases for 3 of those conditions

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Shewanella oneidensis MR-1

Project description:shewanella oneidensis Raw sequence reads

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Shewanella oneidensis MR-1

Project description:Shewanella oneidensis MR-1 Transcriptome or Gene expression

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Transcriptional targets of Shewanella oneidensis HnoC (SO_2540)

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

2013-11-01 | E-GEOD-44689 | biostudies-arrayexpress

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