From GEO Summary: The impact of different carcinogenic exposures on the specific patterns of somatic mutations in human tumors remains unclear. To clarify this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by liver fluke Opisthorchis viverrini (OV)-infection and 101 cases due to non-OV etiologies. Whole-exome (N = 15) and prevalence screening (N...

TCGA Kidney Renal Clear Cell Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. his dataset contains summary data visualizations and clinical data from a broad sampling of 538 carcinomas from 537 patients. The data was gathered as part of the Broad Institute of MIT and Harvard Firehose initiative, a cancer analysis pipeline. The clinical data includes mutation count,...

Summary from the GEO: "Cancer evolution is fueled by genetic and epigenetic diversity, and intra-tumoral heterogeneity in DNA methylation has been shown to co-operate with genetic heterogeneity to empower evolutionary capacity of cancers such as chronic lymphocytic leukemia. Here, we show that epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely...

Summary from the GEO: "The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently...

Summary from the GEO: "Heterochromatin-specific histone modifications frequently coexist with mammalian DNA methylation to orchestrate a repressive chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, we report that the first bromoadjacent homology (BAH1) domain and the replication foci targeting sequence (RFTS) of maintenance DNA methyltransferase DNMT1...

Summary from the GEO:"Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone lysine 20 (H4K20me3) in pluripotency and development are largely unknown. Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin...

Summary from the GEO: "Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone lysine 20 (H4K20me3) in pluripotency and development are largely unknown. Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin...

Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Summary: This SuperSeries is composed of the SubSeries GSE94033 and GSE94085. Article summary that correlates to the GEO: "Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive...

This SuperSeries is composed of the following SubSeries: GSE107024 Intervals of unmethylated DNA spatially co-segregate in cis and in trans [WGBS] GSE107147 DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq] GSE107148 DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC] GSE107149...

Summary from the GEO: "High order chromatin structure and DNA methylation are implicated in multiple development processes and diseases. Despite the recent developments of methods studying high order chromatin interactions, how DNA methylation is associated with high order chromatin structure is not clear. Currently, it is believed that the insulator protein CTCF binding is blocked by DNA methylation,...