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Title: Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing      
dateReleased:
09-01-2012
description:
High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks including nucleotide sequence extraction, alignment, quantification, normalization and visualization. Importantly, Xpression supports multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls p-coumarate degradation by the bacterium Rhodopseudomonas palustris. Comparison of wild-type vs. couR mutant RNA-seq data to identify genes regulated by CouR. 2 wild-type replicates, 1 couR mutant replicate.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-39025
refinement:
raw
alternateIdentifiers:
39025
keywords:
functional genomics
dateModified:
11-06-2012
availability:
available
types:
gene expression
name:
Rhodopseudomonas palustris CGA009
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-39025/E-GEOD-39025.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-39025/E-GEOD-39025.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39025
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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