Ptf1a and RbpjL ChIP-seq in mouse pancreas
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ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR707108.fastq.gz | Fastqsanger.gz | |||
| ERR707109.fastq.gz | Fastqsanger.gz | |||
| ERR707110.fastq.gz | Fastqsanger.gz | |||
| ERR707111.fastq.gz | Fastqsanger.gz | |||
| ERR707112.fastq.gz | Fastqsanger.gz |
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Project description: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.
2014-12-23 | E-MTAB-3197 | biostudies-arrayexpress
Project description:RNA-seq analysis documented mRNA changes in total pancreatic RNA preparations 14 days after Ptf1a inactivation. pancreas mRNA profiles of Tamoxifen treated adult control mice [Ptf1a(CreER/+)] and Ptf1a conditional knockout mice [Ptf1a(CreER/fl)] were generated by deep sequencing using an Illumina Hiseq 2500.
2015-07-22 | E-GEOD-70542 | biostudies-arrayexpress
Project description:The Ptf1a gene has essential functions during several stages of pancreas development. It is expressed in the naïve 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.
2012-11-01 | GSE34193 | GEO
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.
2012-11-01 | E-GEOD-34193 | biostudies-arrayexpress
Project description:Ptf1a was identified as the essential transcription factor which controls pancreatic exocrine enzyme expression. With lineage tracing eperiments Ptf1a was recognized as an important pancreatic progenitor transcription factor and Ptf1a null mice do not develop a pancreas. We used gene expression arrays to determine the global differeences in expression levels when pancreatic progenitor cells are expanding in Ptf1a heterozygote versus null mutants at E10.5. Ptf1a E10.5 dorsal pancreas total RNA from pools of 3 embryos was twice linear amplified and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 in triplicate for the Ptf1a KO and in duplicate for the Ptf1a heterozygote
2011-01-24 | E-GEOD-26816 | biostudies-arrayexpress
Project description:Ptf1a is a lineage-specific basic-helix-loop-helix transcription factor critical in the development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. A majority of regions bound by Ptf1a are tissue-specific, lie near genes needed for proper formation and maturation of each tissue, and reflect regions of open chromatin. Information for the specificity of Ptf1a binding and function is encoded in the DNA surrounding the Ptf1a-bound sites, since Ptf1a-bound regions are sufficient to direct tissue-restricted reporter expression when tested in transgenic mice. Fox and Sox factors were identified as lineage specific modifiers of Ptf1a binding, since binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Although Ptf1a and Foxa2 co-localize to sites in embryonic pancreas and can act synergistically in cell transfection assays, biochemical experiments detected no physical interaction between the two factors. These findings indicate that lineage-specific chromatin landscapes likely constrain the functions of Ptf1a, and identify Fox and Sox gene families as part of this process.
2013-08-15 | GSE47459 | GEO
Project description:Ptf1a is a lineage-specific basic-helix-loop-helix transcription factor critical in the development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. A majority of regions bound by Ptf1a are tissue-specific, lie near genes needed for proper formation and maturation of each tissue, and reflect regions of open chromatin.M-BM- M-BM- Information for the specificity of Ptf1a binding and function is encoded in the DNA surrounding the Ptf1a-bound sites, since Ptf1a-bound regions are sufficient to direct tissue-restricted reporter expression when tested in transgenic mice. Fox and Sox factors were identified as lineage specific modifiers ofM-BM- Ptf1a binding, sinceM-BM- binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Although Ptf1a and Foxa2 co-localize to sites in embryonic pancreas and can act synergistically in cell transfection assays, biochemical experiments detected no physical interaction between the two factors. These findingsM-BM- indicateM-BM- that lineage-specific chromatin landscapes likely constrain the functions of Ptf1a, and identify Fox and Sox gene families as part of this process. RNA-Seq: Examination of gene expression in Ptf1a expressing cells (NT E.12.5, Pancreas E15.5) ChIP-Seq: Examination of chromatin occupancy in 2 tissue types (E12.5 NT and 17.5 Pancreas). Faire-Seq: Examination of open chromatin in 2 tissue types (E12.5 NT and 17.5 Pancreas).
2013-08-15 | E-GEOD-47459 | biostudies-arrayexpress
Project description:This experiment used RNA-Seq technology to explore gene expression in mouse Ptf1a^YFP/+ [het] FACS sorted cells at E11.5 (early pancreatic Multipotent Progenitor Cells) and E15.5 (nascent acinar cells) as well as in Ptf1a^YFP/YFP [null] at E11.5 (delayed early MPC). 376 selected genes identified as differentially expressed between early pancreatic MPC and nascent acinar cells or between early pancreatic and delayed early MPCs have then been examined by Taqman Low Density Arrays (TLDAs) with Real Time RT-PCR for each 1-day time point from E10.5 to E15. 5 in Ptf1a^YFP/+ [het] and for E10.5 and E11.5 in Ptf1aYFP/YFP [null] . Finally, 94 genes identified in the first phase of TLDAs (including 2 endogenous control, Gapdh and 18S) were analyzed in a second TLDA phase for each 1-day time point from E10.5 to -E18.5 in Ptf1a^YFP/+ [het] and for E11.5 in Ptf1aYFP/YFP [null] with biological replicates (n>=3) for each time point.
2014-11-15 | E-MTAB-449 | biostudies-arrayexpress
Project description:We first used RNA-Seq technology to explore gene expression in mouse Ptf1a^YFP/+ [het] FACS sorted cells at E11.5 (early pancreatic Multipotent Progenitor Cells) and E15.5 (nascent acinar cells) as well as in Ptf1a^YFP/YFP [null] at E11.5 (delayed early MPC): this is deposited with accession number E-MTAB-449. We then examined 376 selected genes identified as differentially expressed between early pancreatic MPC and nascent acinar cells or between early pancreatic and delayed early MPCs by Taqman Low Density Arrays (TLDAs) with Real Time RT-PCR for each 1-day time point from E10.5 to E15. 5 in Ptf1a^YFP/+ [het] and for E10.5 and E11.5 in Ptf1aYFP/YFP [null] . Finally, 94 genes identified in the first phase of TLDAs (including 2 endogenous control, Gapdh and 18S) were analyzed in a second TLDA phase for each 1-day time point from E10.5 to -E18.5 in Ptf1a^YFP/+ [het] and for E11.5 in Ptf1aYFP/YFP [null] with biological replicates (n>=3) for each time point.
2014-11-15 | E-MTAB-2780 | biostudies-arrayexpress
Project description:Significant progress has been made in recent years in characterizing human multipotent progenitor cells (hMPCs) of the early pancreas; however, the identity and persistence of these cells during the second trimester, after the initiation of branching morphogenesis, remain elusive. Additionally, studies on hMPCs have been hindered by few isolation methods that allow for the recovery of live cells. Here, we investigated the tip progenitor domain in the branched epithelium of human fetal pancreas between 13.5 and 17.5 gestational weeks by immunohistological staining. We also used a novel RNA‐based technology to isolate live cells followed by gene expression analyses. We identified cells co‐expressing SOX9 and PTF1A, two transcription factors known to be important for pancreatic MPCs, within the tips of the epithelium and observed a decrease in their proportions over time. Pancreatic SOX9+/PTF1A+ cells were enriched for MPC markers, including MYC and GATA6. These cells were proliferative and appeared active in branching morphogenesis and matrix remodeling, as evidenced by gene set enrichment analysis. We identified a hub of genes pertaining to the expanding tip progenitor niche, such as FOXF1, GLI3, TBX3, FGFR1, TGFBR2, ITGAV, ITGA2, and ITGB3. YAP1 of the Hippo pathway emerged as a highly enriched component within the SOX9+/PTF1A+ cells. Single‐cell RNA‐sequencing further corroborated the findings by identifying a cluster of SOX9+/PTF1A+ cells with multipotent characteristics. Based on these results, we propose that the SOX9+/PTF1A+ cells in the human pancreas are uncommitted MPC‐like cells that reside at the tips of the expanding pancreatic epithelium, directing self‐renewal and inducing pancreatic organogenesis.
2019-11-27 | GSE141087 | GEO