Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Ptf1a and RbpjL ChIP-seq in mouse pancreas

ABSTRACT: Ptf1a and RbpjL form a complex. We wanted to identify genes that are regulated by the complex and distinguish those possibly regulated independently by Ptf1a and RbpjL in mouse pancreas using ChIP-seq technology. Chromatin Immunoprecipitations (ChIPs) for Ptf1a and RbpjL were performed with a number of mouse pancreas samples. Samples were sequenced with Solexa and sequenced DNA from Input (n=2), Ptf1a ChIP (n = 3), and RbpjL ChIP (n=2) samples were aligned to the NCBI Genome Build 37 M-^V mm9 to determine regions that were enriched for binding by Ptf1a and RbpjL.

INSTRUMENT(S): Illumina Genome Analyzer

ORGANISM(S): Mus musculus

SUBMITTER: Ray MacDonald

PROVIDER: E-MTAB-3197 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Replacement of Rbpj with Rbpjl in the PTF1 complex controls the final maturation of pancreatic acinar cells.

Masui Toshihiko T Swift Galvin H GH Deering Tye T Shen Chengcheng C Coats Ward S WS Long Qiaoming Q Elsässer Hans-Peter HP Magnuson Mark A MA MacDonald Raymond J RJ

Gastroenterology 20100414 1

<h4>Background & aims</h4>The mature pancreatic acinar cell is dedicated to the production of very large amounts of digestive enzymes. The early stages of pancreatic development require the Rbpj form of the trimeric Pancreas Transcription Factor 1 complex (PTF1-J). As acinar development commences, Rbpjl gradually replaces Rbpj; in the mature pancreas, PTF1 contains Rbpjl (PTF1-L). We investigated whether PTF1-L controls the expression of genes that complete the final stage of acinar differentiat ...[more]

PMID: 20398665

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Project description:The Ptf1a gene has essential functions during several stages of pancreas development. It is expressed in the naM-CM-/ve endoderm and required pancreas cell fate specification; it is also required later in the differentiation and maintenance of acinar cells. To identify the regulatory genetic program downstream of Ptf1a required for early pancreatic fate acquisition, we used microarrays to perform a comprehensive gene expression analysis of Ptf1a overexpressing endodermal tissue at NF32 and NF36. The results revealed an up-regulation on 1142 probe sets over 2-fold. Additional analyses, by in situ hybridizations, identified 9 genes that were endodermally expressed after the onset of endogenous Ptf1a; STXBP1, putative transmembrane protein TA-2, C25H, IGFBP1, IRF1, HALPN3, Hey1, sestrin 1, syndecan-4. These results provide insight into the regulatory network activated by Ptf1a during early pancreas development. In order to identify downstream targets of Ptf1a, two microarrays were performed at different time-points. The two microarrays compared control pancreatic tissue (GFP) and pancreatic tissue over-expressing Ptf1a (Ptf1a+GFP). The first microarray was performed at NF32, hence renamed MA32, 8 hours after the initial expression of endogenous Ptf1a. A second microarray was performed at NF36 (MA36), 8 hours after the first one. Ptf1a+gfp mRNA or gfp mRNA alone was injected into the two dorso-vegetal blastomeres of eight-cell embryos, targeting the anterior endoderm, and 40/48 hours later the anterior endoderm was dissected out. Approximated 15 endoderm explants were pooled for each RNA preparation, and both control and experimental samples were collected from the same batch of embryos; this was done in triplicate at NF32 and in quadruplicate at NF36 (Fig. 1A). For the NF32 microarray, we used the Affymetrix 3M-bM-^@M-^Y Xenopus laevis Genome 2.0 GeneChip, whereas for the NF36 microarray we used the Affymetrix 3M-bM-^@M-^Y Xenopus laevis Genome 1.0 GeneChip; the NF36 microarray was performed prior to the release of the 2.0 GeneChip.

Dataset Information

Ptf1a and RbpjL ChIP-seq in mouse pancreas

Publications

Replacement of Rbpj with Rbpjl in the PTF1 complex controls the final maturation of pancreatic acinar cells.

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