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| Status |
Public on Jul 28, 2016 |
| Title |
RNAseq analysis of the duodenum of intestine-specific adult TN mutant mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/TN;Villin-Cre (TNint) 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: 299 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones.
Conclusion: The TN domain of Nkx2.2 regulates specification of some enteroendocrine cells
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| Overall design |
mRNA profiles of the duodenum of 6 week old control and TNint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
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| Contributor(s) |
Gross S, Sussel L |
| Citation(s) |
27287799 |
| |
| Submission date |
Sep 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lori Sussel |
| E-mail(s) |
lori.sussel@cuanschutz.edu
|
| Organization name |
University of Colorado
|
| Street address |
1775 Aurora Ct.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA295013 |
| SRA |
SRP063412 |
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