Project description:To investigate enhancers and super-enhancers in liver cancer cells, we performed H3K27ac ChIP-seq in SK-Hep-1, Huh7, SNU387, and SNU182 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.
Project description:To explore the m6a modification in SK-Hep-1 cells, we performed RNA immunoprecipitation with an antibody against m6a (SYSY), and sequencing was performed using Illumina NovaSeq 6000
Project description:The openness of chromatin affects the expression and regulation of genes. In order to figure out the changes of transcriptional factors after sirolimus treatment in hepatocellular carcinoma, ATAC-seq was performed for human hepatocellular carcinoma cell line SK-HEP-1. Here, we found that a series of transcriptional factors, including E2F1, SP1, M2F1, etc. enhanced binding to DNA after sirolimus treatment.
Project description:H3K27ac 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
Project description:Emerging evidences indicate that microRNAs (miRNAs) are often deregulated and have fundamental roles in hepatocellular carcinoma (HCC). However, the mechanism underlying miRNA dysregulation in HCC is still elusive. In this report, we used an integrated analysis strategy combining methylated DNA immunoprecipitation chip (MeDIP-chip) and miRNA expression microarray data to study the correlation between aberrant methylation and dysregulation of miRNA in HCC. In all, we showed that global miRNA methylation profiles were significantly different between cancerous and normal hepatocytes, and abnormal methylation was an important mechanism governing miRNA expression in HCC. MeDIP-chip was processed in cancerous hepatocytes SK-HEP-1, HepG2, MHCC97-H and normal hepatocytes PHHC-4-1, PHHC-4-2, PHHC-4-3 (3 technical repeat of PHHC-4). MiRNA microarray were processed for cancerous hepatocytes SK-HEP-1, HepG2, Hep3B, Huh7, MHCC97-H, MHCC97-L, SMMC-7721 and normal hepatocytes PHHC-1, PHHC-2, PHHC-3. Then an integrated analysis strategy combining MeDIP-chip and miRNA expression microarray [GSE20077] were used to study the correlation of aberrant DNA methylation and dysregulation of miRNAs.
Project description:ChIP-seq against H3K27ac using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903). 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