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Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts

ABSTRACT: Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts

PROVIDER: PRJNA322033 | ENA |

REPOSITORIES: ENA

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Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [RNA-seq]

Project description:Polycomb-mediated gene repression plays an important role in adult stem cell maintenance. We knocked out (using the inducible AhCre-LoxP system) Polycomb genes Eed and Ezh2 in the intestine for 6 weeks, after which crypts - the small intestinal stem cell zone - were harvested and RNA sequenced. We found Wnt, Notch and cell cycle pathways to be affected in Eed knockout (KO) but not Ezh2 KO crypts. Direct targets of Eed were determined by comparing this data with ChIP-sequencing. Small intestinal crypt mRNA profiles of 6 weeks-induced 12 weeks old Eed KO, Ezh2 KO and WT mice (all triplicates) as well as 10 days-induced Eed KO and WT organoids (duplicates) were generated by RNA sequencing over two runs and using IlluminaHiseq2000 and Hiseq2500.

2016-07-01 | E-GEOD-81576 | biostudies-arrayexpress

Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [RNA-seq]

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Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [ChIP-seq]

Project description:Polycomb-mediated gene repression plays an important role in adult stem cell maintenance. Direct targets of the Polycomb repressive complex PRC2 in th intestinal epithelium were revealed by performing ChIP-sequencing on crypt samples isolated from wild type murine small intestines. The resulting list of H3K27me3-enriched genes were compared with RNA-sequencing data from wild type and Eed knockout crypts. Crypts were isolated from wild type murine intestinal epithelium and subjected to ChIP using anti-H3K27me3 and anti-H3K27Ac antibodies, after which DNA isolated from extracted immunocomplexes was sequenced.

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Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [ChIP-seq]

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Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-07-01 | E-GEOD-81578 | biostudies-arrayexpress

Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts

Project description:This SuperSeries is composed of the SubSeries listed below.

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Eed conditional knockout in chondrocytes

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Transcriptomic profiling of small intestinal crypts upon MEX3A deletion

Project description:The effort to better understand intestinal stem cell (ISC) identity and regulation remains a challenge. We have been studying the RNA-binding protein MEX3A as a putative ISC marker. In that context, we have generated the first Mex3a knockout (KO) mouse model and show MEX3A is crucial for maintenance of the Lgr5+ ISC pool. As part of a phenotypic characterization pipeline, we have performed transcriptomic profiling (RNA-sequencing) of isolated Mex3a KO small intestinal crypts and compared it against small intestinal crypts isolated from age-matched wild-type controls.

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