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Expression analysis of sk-hep-1(sk) cell and sk-hep-1-sh EZH2(sks) cell

ABSTRACT: Investigation of EZH2 knocking down on whole genome gene expression level changes in sk-hep-1 compared to sk-hep-1-sh EZH2.

ORGANISM(S): Homo sapiens

PROVIDER: GSE68863 | GEO | 2015/08/13

SECONDARY ACCESSION(S): PRJNA284103

REPOSITORIES: GEO

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

Project description: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.

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SK-N-SH Hi-C

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SNP array of human neuroblastoma cell lines SH-SY5Y, SH-EP and SK-N-SH

Project description:TERT promoter muatations occur frequently in tumors of various origin. We here accessed the frequency of TERT pomoter mutations in 131 human primary neuroblastomas and 20 human neuroblastoma cell lines. No TERT promoter mutations were found in the 131 primary neuroblastomas. However, in the three cell lines SH-SY5Y, SH-EP and SK-N-SH a TERT promoter mutation was detected. Sanger sequencing indicated a homozygous mutation. To confirm loss of heterozygosity (LOH) we performed Affymetrix CytoScanHD SNP arrays. Indeed LOH could be confirmed. SNP arry experiments were performed according to the standard protocol for Affymetrix CytoScanHD arrays (Affymetrix, Santa Clara). Briefly, a 250 ng sample of genomic DNA was digested with NspI, ligated to adaptors, amplified by PCR, fragmented and biotin-labeled. The labeled samples were hybridized to Affymetrix CytoscanHD arrays, followed by washing, staining and scanning in the Affymetrix GeneChip Scanner 3000. Analysis was performed using the Affymetrix Chromosome Analysis Suite v2.1.

2015-03-03 | E-GEOD-66422 | biostudies-arrayexpress

Homo sapiens

Project description:Expression analysis of sk-hep-1(sk) cell and sk-hep-1-sh EZH2(sks) cell

| PRJNA284103 | ENA

ChIP-seq from SK-N-SH (ENCSR000FCT)

Project description:H3K9me3 SK-N-SH ChIP-Seq For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-10-14 | GSE86671 | GEO

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