|
| Status |
Public on Jan 24, 2012 |
| Title |
MDA-T, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB231 Treated
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: treatment with DAC
|
| Treatment protocol |
Cells were seeded (2 X l0^5 cells / T75 flasks) for 24h then media were removed and cells were freshly exposed to the 5-aza-2’-deoxycytidine (DAC) (Sigma Chemical Co.) at concentrations of l00nM in suspension culture every 24h until cultured cells reached 80-85 % confluence (~5 days). The cells were split for 10 follow-up passages at “drug holiday” condition.
|
| Growth protocol |
HB2 cell line was cultured in DMEM, 10% FBS, Insulin (0.01 mg/ml, hydrocortisone (500 ng/ml). MDA-MB231 cell line was cultured in DMEM, 10% FBS. SKBR3 cell line was cultured in McCoys 5A, 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN AG) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated mRNAs were prepared according to the FlashTag Biotin HSR RNA Labeling protocol (Genisphere) using 100ng total RNA.
|
| |
|
| Hybridization protocol |
The labelled products were hybridized for 18 hr at 45C on Affymetrix Genome 133 Plus 2.0 GeneChips. GeneChips were washed and stained on GeneChip Fluidics 450 Workstations (Affymetrix Inc.).
|
| Scan protocol |
The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.)
|
| Description |
Gene expression data directly after treatment with DAC
|
| Data processing |
The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software v6.5 (Partek Incorporated, Missouri, USA) and and RMA normalization.
|
| |
|
| Submission date |
Apr 29, 2011 |
| Last update date |
Jan 24, 2012 |
| Contact name |
Ramin Radpour |
| Organization name |
University of Bern
|
| Department |
Department for BioMedical Research
|
| Street address |
Murtenstrasse 35
|
| City |
Bern |
| ZIP/Postal code |
3008 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL8019 |
| Series (2) |
| GSE28968 |
MRNA expression data from human breast cancer cell lines after demethylation treatment. |
| GSE28976 |
Expression data from human breast cancer cell lines after demethylation treatment |
|
