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Title: RNAseq analysis of the duodenum of intestine-specific adult Nkx2.2 mutant mice      
dateReleased:
07-28-2016
description:
Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) 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: 184 genes with a p-value <0.05 were down-regulated and 211 were up-regulated. Among the down-regulated genes are most enteroendocrine hormones. Conclusion: Nkx2.2 regulates enteroendocrine cell specification mRNA profiles of the duodenum of 6 week old control and Nkx2.2int mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-72761
refinement:
raw
alternateIdentifiers:
72761
keywords:
functional genomics
dateModified:
07-29-2016
availability:
available
types:
gene expression
name:
Mus musculus
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-72761/E-GEOD-72761.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-72761/E-GEOD-72761.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=GSE72761
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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