Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Lori Sussel 

PROVIDER: E-GEOD-78902 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The novel enterochromaffin marker Lmx1a regulates serotonin biosynthesis in enteroendocrine cell lineages downstream of Nkx2.2.

Gross Stefanie S   Garofalo Diana C DC   Balderes Dina A DA   Mastracci Teresa L TL   Dias José M JM   Perlmann Thomas T   Ericson Johan J   Ericson Johan J   Sussel Lori L  

Development (Cambridge, England) 20160610 14

Intestinal hormone-producing cells represent the largest endocrine system in the body, but remarkably little is known about enteroendocrine cell type specification in the embryo and adult. We analyzed stage- and cell type-specific deletions of Nkx2.2 and its functional domains in order to characterize its role in the development and maintenance of enteroendocrine cell lineages in the mouse duodenum and colon. Although Nkx2.2 regulates enteroendocrine cell specification in the duodenum at all sta  ...[more]

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