Genomics

Dataset Information

46

Genome-wide maps of H3K27me3 modification sites in sk-hep-1,sk-hep-1-shEZH2 and LO2 cells.


ABSTRACT: We report the application of chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) for high-throughput profiling of H3K27me3 modifications in sk-hep-1(sk), sk-hep-1-shEZH2 (sks) and LO2 cells. Following standard ChIP procedure, 10 ng of each DNA sample was used for Illumina sequencing. Statistically significant ChIP-enriched regions (peaks) were identified by sk vs sks (p-value threshold of 10-2) or sk vs LO2 (p-value threshold of 10-3). Enriched peaks were annotated by the nearest gene using the newest UCSC RefSeq database. We identify genes modified by EZH2-mediated H3K27me3. This study provides insights into these down stream genes modified by EZH2 regulated H3K27me3 in HCC cell lines. Overall design: Examination of H3K27me3 in 3 HCC cell lines.

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

SUBMITTER: Li Changpeng 

PROVIDER: GSE68758 | GEO | 2015-08-13

SECONDARY ACCESSION(S): PRJNA283798

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE68758_RAW.tar Raw
GSE68758_SK_vs_LO2_broad_peaks.bed.gz Bed
GSE68758_SK_vs_LO2_peaks.xls.gz Xls
GSE68758_SK_vs_SKS_broad_peaks.bed.gz Bed
GSE68758_SK_vs_SKS_peaks.xls.gz Xls
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Publications

CLDN14 is epigenetically silenced by EZH2-mediated H3K27ME3 and is a novel prognostic biomarker in hepatocellular carcinoma.

Li Chang-Peng CP   Cai Mu-Yan MY   Jiang Li-Juan LJ   Mai Shi-Juan SJ   Chen Jie-Wei JW   Wang Feng-Wei FW   Liao Yi-Ji YJ   Chen Wen-Hui WH   Jin Xiao-Han XH   Pei Xiao-Qing XQ   Guan Xin-Yuan XY   Zeng Mu-Sheng MS   Xie Dan D  

Carcinogenesis 20160331 6


Trimethylation of lysine 27 on histone H3 (H3K27ME3) is a transcription-suppressive histone mark mediated by enhancer of zeste homolog 2 (EZH2). We have previously suggested that EZH2-mediated H3K27ME3 plays a critical oncogenic role in human hepatocellular carcinoma (HCC) aggressiveness. However, the direct downstream targets of EZH2-H3K27ME3 and the molecular mechanisms by which regulates HCC pathogenesis remain unclear. In this study, we used chromatin immunoprecipitation together with high-t  ...[more]