|
| Status |
Public on Jan 09, 2017 |
| Title |
RNA-Seq analysis of E15.5 pancreas of both whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Aim: Transcriptional analysis of E15.5 whole pancreas of Nkx2.2-LacZ/LacZ embryos versus control and Ngn3-Cre; Nkx2.2-flox/flox embryos versus control
Methods: Embryonic pancreata were isolated at E15.5 from Nkx2.2 mutant mice and controls. Total RNA was 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: There is significant overlap between the differentially expressed genes of whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos; many of the downregulated genes (p-value < 0.05) are genes involved in beta cell function.
Conclusion: Nkx2.2 functions within the endocrine progenitor lineage to activate beta cell genes
|
| |
|
| Overall design |
mRNA profiles of whole embryonic pancreata of E15.5 Nkx2.2 mutant and control embryos were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
|
| |
|
| Contributor(s) |
Churchill AJ, Sussel LG |
| Citation(s) |
28071588 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DK082590 |
Regulation of pancreatic cell fate |
UNIVERSITY OF COLORADO DENVER |
LORI SUSSEL |
|
| |
| Submission date |
Apr 19, 2016 |
| Last update date |
Sep 12, 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 |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA318911 |
| SRA |
SRP073503 |
Less...
More...