|
| Status |
Public on Oct 21, 2014 |
| Title |
NCCIT_siRNA_DNMT3B (biological replicate 3) |
| Sample type |
genomic |
| |
|
| Source name |
DNA from NCCIT human cells depleted of DNMT3B by siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: embryonic carcinoma cells
transfected with: siRNA against DNMT3B
|
| 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 |
DNMT3B-2
NCCIT human cells depleted of 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.
|
| |
|
| Submission date |
Oct 17, 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 |
|
