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
|