Project description:We described a new culture system that can expand the developmental potential of pluripotent stem cells to contribute efficiently to extraembryonic lineage development. To compare the epigenetic landscape of expanded potential stem cells (EPSCs) and standard embryonic stem cells, we performed ChIP-seq study on multiple histone modifications to establish the epigenetic landscape of EPSCs.

2015-09-09 | E-ERAD-426 | biostudies-arrayexpress

The epigenetic landscape of human colorectal cancer

Project description:We characterized the epigenetic landscape of human colorectal cancer (CRC). To this extent, we performed gene expression profiling using high throughput sequencing (RNA-seq) and genome wide binding/occupancy profiling (ChIP-seq) for histone modifications correlated to transcriptional activity, enhancers, elongation and repression (H3K4me3, H3K4me1, H3K27Ac, H3K36me3, H3K27me3) in patient-derived organoids (PDOs), and in normal and tumoral primary colon tissues. We also generated ChIP-seq data for transcription factors YAP/TAZ in human CRC PDOs.

2021-02-23 | E-MTAB-8416 | biostudies-arrayexpress

The epigenetic landscape of human colorectal cancer

2021-03-10 | E-MTAB-8448 | biostudies-arrayexpress

The epigenetic landscape of human colorectal cancer - 10x dataset

Project description:The epigenetic landscape of human colorectal cancer - 10x dataset

| PRJEB40272 | ENA

Integrating 5 Hydroxymethylcytosine into the Epigenetic Landscape of Human Embryonic Stem Cells

Project description:Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC. Genome wide enrichment profile of 5-hmC in H1 human embryonic stem cells

2011-06-24 | E-GEOD-30173 | biostudies-arrayexpress

Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms (snMultiome)

Project description:Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms

2022-01-10 | GSE178453 | GEO

Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms (snATAC-seq)

Project description:Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms

2022-01-10 | GSE178451 | GEO

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