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Series GSE84399 Query DataSets for GSE84399
Status Public on Jan 01, 2017
Title Analysis of DNA methylation in TET1 depleted colorectal cancer HCT116 cells
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary 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.
 
Contributor(s) Suzuki H
Citation(s) 27977763
Submission date Jul 14, 2016
Last update date Mar 22, 2019
Contact name Hiromu Suzuki
E-mail(s) hsuzuki@sapmed.ac.jp
Phone +81-11-611-2111
Organization name Sapporo Medical University
Department Department of Molecular Biology
Street address S1, W17, Chuo-ku
City Sapporo
State/province Hokkaido
ZIP/Postal code 060-8556
Country Japan
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (4)
GSM2233046 HCT116 control #1 [DNA methylation]
GSM2233047 HCT116 control #2 [DNA methylation]
GSM2233048 HCT116 TET1-knockdown #1 [DNA methylation]
This SubSeries is part of SuperSeries:
GSE84400 Analysis of DNA methylation and gene expression in TET1 depleted colorectal cancer cells
Relations
BioProject PRJNA329084

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE84399_9426020105_R06C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSE84399_9426020105_R06C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
GSE84399_9426021173_R03C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSE84399_9426021173_R03C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
GSE84399_RAW.tar 183.1 Mb (http)(custom) TAR
GSE84399_non_normalized.txt.gz 10.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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