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Title: RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice      
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available
aggregation:
instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
07-28-2016
ID:
E-GEOD-78902
description:
Aim: Transcriptional analysis of the colon of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the colon (as measured after the caecum) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq. Results: 53 genes with a p-value <0.05 were down-regulated and 36 were up-regulated. Among the changed genes are enteroendocrine hormones. Conclusion: Nkx2.2 regulates enteroendocrine cell specification mRNA profiles of the colon of 6 week old control and Nkx2.2int mice were generated by deep sequencing, using Illumina HiSeq2000.
keywords:
RNA-seq of coding RNA
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HTML
storedIn:
Array Express
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primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-78902
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JSON
storedIn:
OmicsDI
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accessType:
download
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false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-78902.json
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XML
storedIn:
OmicsDI
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not compressed
accessType:
download
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none
authentication:
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primary:
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accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-78902.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/