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Title: Transcription profiling by high throughput sequencing of Arabidopsis roots under iron or phosphate stress      
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available
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instance of dataset
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not applicable
refinement:
curated
dateReleased:
02-11-2016
ID:
E-MTAB-4472
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.
keywords:
RNA-seq of coding RNA
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HTML
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Array Express
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landing page
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primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4472
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JSON
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OmicsDI
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accessType:
download
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false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-MTAB-4472.json
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XML
storedIn:
OmicsDI
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not compressed
accessType:
download
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none
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primary:
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accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-MTAB-4472.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/