Project description:Methylation analysis of normal lymphocytes, HCT116, RKO and SW480 In vitro methylated DNA (IVD) generated from normal lymphocytes, HCT116, RKO and SW480 genomic DNA was subjected to sodium bisulfite treatment and the DNA was analyzed for CpG methylation using the Infinium Methylation Array.
Project description:DNA hypermethylated genes undergo silencing and show re-expression in response to 5-Aza-CdR treatment. Agilent arrays were used to determine the genes that get reactivated in response to the drug treatment. To determine expression levels of genes in SW480, HCT116 and RKO.
Project description:The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types, however the effects of mutations on epigenome organization, gene expression and cell growth are not clear. To study effects of KMT2C expression in CRC cells we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous KMT2C c.8390delA mutant, by gene editing. RNA sequencing was performed to profile gene expression when KMT2C was restored in RKO and HCT116 cells.
Project description:To investigate the function of CYP1B1 in the regulation of proliferation process, we established SW480 cells in which target gene has been knocked down by shRNA and established RKO cells in which target gene has been upregulated by overexpressed plasmid.
Project description:In microarray analysis, combinational treatment with PJ-34 and 5-aza-dC caused dissimilar broad changes in gene expression profiles compared with their single treatments in both HCT116 and RKO cells. Profiles of reactivation of silenced genes were also different in combination of PJ-34 and 5-aza-dC and their single treatments. The results suggest that combinational use of 5-aza-dC and PARP inhibitor may be useful by causing distinct transcriptional profile changes.
Project description:To explore the mechanisms underlying the radioresistance of colorectal cancer, we established specifically radioresistant HCT116 cell line (HCT116-R cells) and RKO cell line (RKO-R cells) derived from HCT116 and RKO cell lines by repeatedly exposing to multi-fractionated irradiation. Then, the aberrantly expressed miRNA were detected by miRNA sequencing and their bioinformatics were analyzed.
Project description:The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types, however the effects of mutations on epigenome organization, gene expression and cell growth are not clear. To study effects of KMT2C expression in CRC cells we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous KMT2C c.8390delA mutant. Chromatin was analysed by ChIP-sequencing using the Diagenode iDeal ChIP-seq kit for Histones and the H3K4me1 specific antibody (Abcam ab8895).