GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1325002 Query DataSets for GSM1325002
Status Public on Oct 20, 2014
Title HCT116_DNMT1_KO
Sample type genomic
Source name DNA from HCT116 DNMT1 genetic knockout human colorectal carcinoma cells
Organism Homo sapiens
Characteristics cell line: HCT116
cell type: colorectal carcinoma cells
genotype/variation: DNMT1 genetic knockout
Treatment protocol NCCIT cells were transfected (PepMute reagent) with siRNA (Dharmacon) against DNMT expression following the manufacturer's protocol (SignaGen).
Growth protocol NCCIT and HCT116 cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone). HCT116 overexpression cells were selected under G418 (750 µg/ml).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by proteinase K treatment, phenol:chloroform extraction, and ethanol precipitation.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol.
Hybridization protocol Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.
Description 1KO
HCT116 DNMT1 genetic knockout human colorectal carcinoma cells.
Data processing Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi. The 'GSE54840_methylated_unmethylated_signals.txt' file contains methylated and unmethylated signal intensities.
Submission date Feb 10, 2014
Last update date Oct 21, 2014
Contact name Keith D Robertson
Phone 507-266-4886
Organization name Mayo Clinic
Department Molecular Pharmacology & Experimental Therapeutics
Lab Epigenetic Etiology of Human Disease Laboratory
Street address 200 First Street SW, Stabile 12-70
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
Platform ID GPL13534
Series (2)
GSE54840 Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome [methylation]
GSE54843 Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome

Data table header descriptions
VALUE Normalized (SWAN) Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.52450639 0
cg00000108 0.935998547 0
cg00000109 0.894609778 0
cg00000165 0.878582447 0
cg00000236 0.813644585 0
cg00000289 0.540385182 0
cg00000292 0.718567665 0
cg00000321 0.773793428 0
cg00000363 0.852837886 0
cg00000622 0.028722583 0
cg00000658 0.779571778 0
cg00000714 0.152665587 0
cg00000721 0.896789174 0
cg00000734 0.082485064 0
cg00000769 0.09767491 0
cg00000807 0.760509191 0
cg00000884 0.782082096 0
cg00000905 0.070978219 0
cg00000924 0.561333275 0
cg00000948 0.867004671 0

Total number of rows: 485512

Table truncated, full table size 11818 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap