Project description:Heterochromatin conformation is essential for endogenous retroviruses (ERVs) silencing. However, extensive maps of heterochromatin modifications H3K9me2/3 at ERV regions have not yet been provided in human cancer cells. Our ChIP-seq results showed that ERVs tend to be concentrated in regions of heterocromatin, which are marked by the presence of H3K9me3. We also observed dramatic increases H3K9me2/3 in the ERVs after transient treatment with DNA methylation inhibitor.
Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1). The approach is focused on the youngest family (L1HS), but it also catches a significant fraction of L1PA2 to L1PA8 elements. This was performed in HCT116 cells treated by the DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza) or in mock-treated cells (DMSO).
Project description:Genomide DNA methylation profiling of HCT116 cells after PBS, 5-Aza-CdR, vitamin C and combination treatment. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in HCT116 cells.
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:Genome-wide expression and methylation differences are compared for a normal HCT116 cell line and a derived mutant with altered DNA methylation patterns.
Project description:We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established two stable TET1 knockdown clones and negative control clones of HCT116 cells, and carried out DNA methylation analysis with HumanMethylation450 BeadChip.
Project description:Genome-wide expression and methylation differences are compared for a normal HCT116 cell line and a derived mutant with altered DNA methylation patterns. The data compares the effect of a gene mutation on genome-wide expression (and methylation). This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP) Keywords: parental, mutant
Project description:Analysis of cross talk of epigenetic marks in HBEC by using tilling arrays chr19. In Human Bronchial epithelia cells (HBEC), H3K9me3, H4K20me3, H3K4me3, H3K27me3, H3K36me3 and DNA methylation were profiled. In these cells, DNA methylation status was analyzed by MIRA and UnmethylCollector (UMC). Study of epigenetic changes in HCT116 DNMT1-/- and DNMT3b -/- (HCT116-DKO) in comparison to intact HCT116. In HCT116 and HCT116-DKO, H3K9me3, H3K36me3 and DNA methylation were profiled. In these cells, DNA methylation status was analyzed by MIRA. Analysis of epigenetic changes caused by siRNA for SED2 transcript in HBEC. In HBEC and SETD2 siRNA HBEC, H3K36me3 and DNA methylation were profiled. In these cells, DNA methylation status was analyzed by MIRA.
