|
| Status |
Public on Oct 20, 2014 |
| Title |
NCCIT siD1+3A+3B rep1 |
| Sample type |
RNA |
| |
|
| Source name |
NCCIT_DNMT1, DNMT3A, and DNMT3B depletion
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: embryonic carcinoma cells
transfected with: siRNA against DNMT1, DNMT3A, and DNMT3B transcript
genotype/variation: DNMT1, DNMT3A, and DNMT3B depletion
|
| Treatment protocol |
NCCIT cells were transfected (PepMute reagent) with siRNA (Dharmacon) against DNMT expression following the manufacturer's protocol (SignaGen)
|
| Growth protocol |
NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).
|
| |
|
| Hybridization protocol |
Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
D1+3A+3B-1
|
| Data processing |
Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6). Differential expressions were calculated using ANOVA of Partek package.
|
| |
|
| Submission date |
Feb 10, 2014 |
| Last update date |
Sep 01, 2016 |
| 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 |
GPL6244 |
| Series (2) |
| GSE54841 |
Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome [gene expression] |
| GSE54843 |
Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome |
|
| Relations |
| Reanalyzed by |
GSE86357 |
