|
| Status |
Public on Jun 02, 2011 |
| Title |
NC-transfected MCF-7, 12h ETOH |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
condition: NC-transfected MCF-7, ETOH
|
| Treatment protocol |
~400,000 cells were seeded in phenol red-free DMEM/F12 containing 5% charcoal stripped FBS (Hyclone) with penicillin, streptomycin and gentamycin. Within 24h after seeding, cells were transfected with NC or siRNA targeting AP-2γ (from Dharmacon and First Base). Transfection was repeated the next day to achieve double knockdown. After 96h from the first transfection, hormone-depleted cells were treated with E2 to a final concentration of 10 nM for 12h before harvesting for RNA. Cells treated with an equal volume vehicle, ETOH (ethanol) for 12h are used as controls.
|
| Growth protocol |
MCF-7 breast cancer cells were maintained in DMEM (Invitrogen/Gibco) supplemented with 5% fetal bovine serum (FBS), penicillin, streptomycin, and gentamycin in a 37°C incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Sigma) and purified according to manufacturer protocol in PureLink RNA Mini Kit (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 500ng total RNA using Illumina TotalPrep-96 RNA Amplification Kit (Ambion).
|
| |
|
| Hybridization protocol |
750ng of cRNA were hybridized to the Sentrix HumanRef-8 v3 Expression BeadChip Kit (Illumina) according to the manufacturer protocol.
|
| Scan protocol |
BeadChips were scanned using the BeadArray Reader.
|
| Description |
4671881066_F, 4671881068_F, 4671881069_F
|
| Data processing |
Raw data was analyzed using GeneSpring GX 11.0 software. Dataset was normalized using percentile shift normalization and baseline transformed to median of control samples.
Triplicates were generated for the experiment and analyses were performed using the average of the triplicates (after normalization). Raw data provided as supplementary file (filename: GSE26740_non-normalized.txt.gz)
|
| |
|
| Submission date |
Jan 20, 2011 |
| Last update date |
Jun 02, 2011 |
| Contact name |
SI KEE TAN |
| E-mail(s) |
tansk99@gis.a-star.edu.sg
|
| Organization name |
Genomic Institute of Singapore
|
| Department |
Cancer biology and Pharmacology
|
| Street address |
60 Biopolis Street #02-01 Genome
|
| City |
Singapore |
| ZIP/Postal code |
Singapore 138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6883 |
| Series (2) |
| GSE26740 |
Activator protein-2γ is a critical determinant of estrogen receptor interactome formation and gene transcription in breast cancer [expression] |
| GSE26741 |
Activator protein-2γ is a critical determinant of estrogen receptor interactome formation and gene transcription in breast cancer |
|
