Genomics

Dataset Information

39

Analysis of DNA methylation in TET1 depleted colorectal cancer HCT116 cells


ABSTRACT: 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. Overall design: RNAi-induced TET1 knockdown was accomplished using a BLOCK-iT Pol II miR RNAi Expression Vector kit (Thermo Fisher Scientific). Two sets of oligonucleotides targeting TET1 were purchased from Invitrogen and ligated into a pcDNA6.2-GW/EmGFP-miR vector (Thermo Fisher Scientific). Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 0.6 mg/ml G418. GFP-positive colonies were isolated, and knockdown efficiencies were analyzed using RT-qPCR.

INSTRUMENT(S): Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)

SUBMITTER: Hiromu Suzuki  

PROVIDER: GSE84399 | GEO | 2017-01-01

SECONDARY ACCESSION(S): PRJNA329084

REPOSITORIES: GEO

altmetric image

Publications


Aberrant DNA methylation is commonly observed in colorectal cancer (CRC), but the underlying mechanism is not fully understood. 5-hydroxymethylcytosine levels and TET1 expression are both reduced in CRC, while epigenetic silencing of TET1 is reportedly associated with the CpG island methylator phenotype. In the present study, we aimed to clarify the relationship between loss of TET1 and aberrant DNA methylation in CRC. Stable TET1 knockdown clones were established using Colo320DM cells, which ex  ...[more]

Similar Datasets

| GSE84398 | GEO
| GSE84396 | GEO
| GSE84397 | GEO
| GSE85613 | GEO
| GSE99949 | GEO
| GSE77399 | GEO
2018-03-31 | E-MTAB-6526 | ArrayExpress
2013-07-18 | E-GEOD-48998 | ArrayExpress
2011-05-16 | E-GEOD-29144 | ArrayExpress
| GSE79564 | GEO