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DNA methylation analysis of cloned HCT116 cells treated with a DNA demethylating drug.

ABSTRACT: DNA methylation analysis of cloned HCT116 cells treated with a DNA demethylating drug.

PROVIDER: PRJNA627908 | ENA |

REPOSITORIES: ENA

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DNA methylation analysis of cloned HCT116 cells treated with a DNA demethylating drug.

Project description:Epigenetic reprogramming using demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen. Low-dose treatment for a prolonged period shows a high therapeutic efficacy, despite its small demethylating effect. Here, we aimed to reveal the mechanisms of how such low-dose treatment shows high efficacy by focusing on epigenetic reprograming at the single-cell level. Single-cell RNA-sequencing of HCT116 cells treated with decitabine (DAC) revealed that up-regulated genes were highly variable at the single-cell level. To analyze functional consequences at the single-cell level, DAC-treated HCT116 cells were cloned. While only partial reduction of methylation levels was observed in bulk cells, complete demethylation of specific cancer-related genes was observed, depending upon clones. For example, p16 was completely demethylated in the H3-32 clone out of 9 clones, and this clone showed slower proliferation than other clones without demethylation. In addition, in this clone, the fraction of cells with tetraploid became much larger, indicating that cellular senescence was induced. These results showed that epigenetic reprogramming of specific cancer-related pathways at the single-cell level is likely to underlie the high efficacy of low-dose DNA demethylating therapy.

2020-10-02 | GSE149255 | GEO

Methylation profiling by array of human cell line HCT116 after treatment with demethylating drugs azacytidine or decitabine.

Project description:array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs azacytidine and decitabine on HCT116 cells for 24 hours

2010-07-01 | E-MTAB-210 | biostudies-arrayexpress

Genome-wide DNA demethylation of HML58-3 (a derivative cell line of HCT116) after treatment of DAC, OR-2003, and OR-2100

Project description:A derivative cell line of HCT116, HML58-3, was established to detect DNA demethylating agents [Okochi-Takada E, Epigenetics. 2018;13:147-55.]. HML58-3 cells were treated with DNA demethylating agents (DAC, OR-2003, and OR-2100). Genome-wide DNA methylation was analyzed using the Infinium Human MethylationEPIC BeadChip.

2019-08-01 | GSE134293 | GEO

scRNA-seq of DAC-treated and mock-treated HCT116.

2021-04-10 | GSE171429 | GEO

Methylation profiling by array of human HCT116 and HL60 cells treated with the demthylating drugs azacytidine and decitabine

Project description:Array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs azacytidine and decitabine on HCT116 and HL60 cells for 24 hours

2010-12-01 | E-MTAB-417 | biostudies-arrayexpress

DNA methylation inhibitor in HCT116

Project description:DNA methylation inhibitor in HCT116

| PRJNA422822 | ENA

Transcription profiling of mouse primary dermal fibroblasts treated with DNA demethylating agent 5-aza-2-deoxycytidine

Project description:Mouse primary dermal fibroblasts were treated with DNA demethylating agent 5-aza-2'-deoxycytidine. The exposure was 5um 5A2dC for 96 hours followed by recovery in normal medium for 24 hours. Three biological replicates were created for both the control and treated populations. Each biological replicate represents a separate derivation of dermal fibroblasts from genetically identical mouse pups aged 0-3 days. Cells reached passage 4 before initiating drug exposure.

2005-01-01 | E-MEXP-701 | biostudies-arrayexpress

DNA methylation abnormal accumulation during cloned TSCs maintaining

Project description:DNA methylation abnormal accumulation during cloned TSCs maintaining

| PRJNA685859 | ENA

Genome-wide gene expression of HML58-3 (a derivative cell line of HCT116) after treatment of DAC (decitabine), OR-2003, and OR-2100

Project description:A derivative cell line of HCT116, HML58-3, was established to detect DNA demethylating agents [Okochi-Takada E, Epigenetics. 2018;13:147-55.]. HML58-3 cells were treated with DNA demethylating agents (decitabine, OR-2003, and OR-2100) or mock. A genome-wide gene expression analysis was performed using SurePrint G3 Human Gene Expression 8 x 60K v2 Microarray.

2019-08-01 | GSE134294 | GEO

DNA methylation abnormal accumulation during cloned TSCs maintaining [RRBS]

Project description:Trophoblast stem cells (TSCs) are derived from the trophoectoderm of blastocysts and maintain ability to self-renewal and differentiation. TSC is a good model to research placenta development in vitro. It will contribute to understanding and improving cloned placentomegaly to compare the transcription and methylation between cloned and natural fertilized embryos throughout TSC derivation process. In the present study, we used SCNT (NT) and SCNT with HDACi treatment (SNT) as cloned groups and natural fertilized (NF) embryos to derive TSCs and chosed 5-time points to peform RNA-seq and RRBS. We found only NT got a barriar in TSC maintenace and both cloned groups exhited abnormal accumulating DNA methylation and it might be resiponsible for some malformations of cloned placentas.

2021-03-01 | GSE163380 | GEO

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