Genomics

Dataset Information

47

RNA-Seq analysis of E15.5 pancreas of both whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos


ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000 (Mus musculus)

SUBMITTER: Lori Sussel  

PROVIDER: GSE80444 | GEO | 2017-01-09

SECONDARY ACCESSION(S): PRJNA318911

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE80444_DEseq_AP013-AP015-AP016_AP011-AP012-AP014_DEG_list.csv.gz Csv
GSE80444_DEseq_AP017-AP018-AP020_AP019-AP021-AP022_DEG_list.csv.gz Csv
GSE80444_RAW.tar Raw
filelist.txt Txt
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