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RNAseq analysis of the duodenum of intestine-specific adult SD mutant mice

ABSTRACT: Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/SD;Villin-Cre (SDint) 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: 206 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones. Conclusion: The SD domain of Nkx2.2 regulates specification of some enteroendocrine cells mRNA profiles of the duodenum of 6 week old control and SDint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

ORGANISM(S): Mus musculus

SUBMITTER: Lori Sussel

PROVIDER: E-GEOD-72762 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNAseq analysis of the duodenum of intestine-specific adult SD mutant mice

Project description:Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/SD;Villin-Cre (SDint) 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: 206 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones. Conclusion: The SD domain of Nkx2.2 regulates specification of some enteroendocrine cells

2016-07-28 | GSE72762 | GEO

RNAseq analysis of the duodenum of intestine-specific adult Nkx2.2 mutant mice

Project 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.

2016-07-28 | E-GEOD-72761 | biostudies-arrayexpress

RNAseq analysis of the duodenum of intestine-specific adult TN mutant mice

Project description: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 mRNA profiles of the duodenum of 6 week old control and TNint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

2016-07-28 | E-GEOD-72764 | biostudies-arrayexpress

RNAseq analysis of the duodenum of intestine-specific adult TN mutant mice

2016-07-28 | GSE72764 | GEO

RNAseq analysis of the duodenum of intestine-specific adult Nkx2.2 mutant mice

2016-07-28 | GSE72761 | GEO

RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice

Project 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.

2016-07-28 | E-GEOD-78902 | biostudies-arrayexpress

RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice

2016-07-28 | GSE78902 | GEO

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

Project description: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

2017-01-09 | GSE80444 | GEO

RNA-Seq analysis of the pancreatic islets of beta cell specific adult Nkx2.2 mutant mice

Project description:Aim:Transcriptional analysis of the pancreatic islets of adult Nkx2.2 flox/flox; RipCre mice versus control Methods:Pancreatic islets from 4week old Nkx2.2 mutant mice and controls were isolated and 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: Among the downregulated genes with a p-value=0.05 are important genes for beta cell function and idenity.Among the upregulated genes with a p-value=0.05 are non beta endocrine hormones. Conclusion: Nkx2.2 activates important beta cell genes and actively represses non beta cell genes

2016-12-20 | GSE79723 | GEO

Global profiling of Nkx2.2 SD-domain mutant pancreas during development and adulthood compared to transcriptional profiling of SD-domain mutant expressing neural progenitors.

Project description:The consolidation of unambiguous cell fate commitment relies on the ability of transcription factors (TFs) to exert tissue-specific regulation of complex genetic networks. The mechanisms by which TFs establish such precise control over gene expression, however, have remained elusive—especially in instances where a single TF operates in two or more discrete cellular systems. In this study, we demonstrate that  cell specific functions of NKX2.2 are driven by the highly conserved NK2-Specific Domain (SD). Mutation of the endogenous NKX2.2 SD domain prevents the developmental progression of beta cell precursors into mature, insulin-expressing beta cells, resulting in overt neonatal diabetes. Within the adult beta cell, the SD domain stimulates beta cell performance through the activation and repression of a subset of NKX2.2-regulated transcripts critical for beta cell function. These irregularities in beta cell gene expression may be mediated via SD domain-contingent interactions with components of the nuclear pore complex. In stark contrast to these pancreatic phenotypes, however, the SD domain is entirely dispensable for the development of NKX2.2-dependent cell types within the CNS. Together, these results reveal a previously undetermined mechanism through which NKX2.2 directs disparate transcriptional programs in the pancreas vs. neuroepithelium.

2024-02-21 | GSE226345 | GEO

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