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Title: Transcription profiling by high throughput sequencing of Arabidopsis roots under iron or phosphate stress      
dateReleased:
08-19-2011
description:
To analyze context-sensitive changes in pre-mRNA splicing pattern and gene expression, we mapped the transcriptome of iron-deficient and iron-sufficient Arabidopsis roots using the RNA-seq technology. RNA-seq data were analyzed with a newly developed software package, RACKJ (Read Analysis & Comparison Kit in Java). Subsets of 460 and 1480 genes were found to be either differentially expressed or affected in their splicing patterns upon iron deficiency. The two groups showed a small, random overlap, indicating that alternative splicing and differential gene expression represent parallel, but potentially interacting regulatory mechanisms. The majority (~95%%) of the context-sensitive alternative splicing events was due to differentially retained introns. Intron retention was mostly repressed in iron-deficient plants, while exon skipping did not show a clear trend in either direction. A comparison with a similar data set for phosphate-deficient plants supported stress-repressed intron retention and revealed nutrient-specific changes of splicing patterns. It is concluded that iron and phosphate deficiency increases splicing fidelity for a subset of transcripts, probably as a means of acclimation to nutrient shortage.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MTAB-4472
refinement:
raw
keywords:
functional genomics
dateModified:
02-11-2016
creators:
Wolfgang Schmidt
availability:
available
types:
gene expression
name:
Arabidopsis thaliana
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4472/E-MTAB-4472.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-MTAB-4472/E-MTAB-4472.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
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