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Status |
Public on Oct 20, 2014 |
Title |
NCCIT_siRNA_3A+3B |
Sample type |
genomic |
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|
Source name |
DNA from NCCIT human cells depleted of DNMT3A and DNMT3B by siRNA
|
Organism |
Homo sapiens |
Characteristics |
cell line: NCCIT cell type: embryonic carcinoma cells transfected with: siRNA against DNMT3A and DNMT3B
|
Treatment protocol |
NCCIT cells were transfected (PepMute reagent) with siRNA (Dharmacon) against DNMT expression following the manufacturer's protocol (SignaGen).
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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.
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|
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Hybridization protocol |
Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
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Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.
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Description |
3A+3B NCCIT human cells depleted of DNMT3A and DNMT3B by siRNA.
|
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.
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Submission date |
Feb 10, 2014 |
Last update date |
Oct 21, 2014 |
Contact name |
Keith D Robertson |
E-mail(s) |
robertson.keith@mayo.edu
|
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 |
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