|
| Status |
Public on Jul 21, 2015 |
| Title |
S2sh7 SMARCA2 BRD MUT biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
H1299_S2sh7 SMARCA2 BRD MUT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1299
cell type: Lung cancer cells
background genotype/variation: containing shRNA targeting to SMARCA2 gene, ATPase domain
genotype/variation: expressing bromodomain mutant SMARCA2
batch: Batch1
|
| Treatment protocol |
none; untreated
|
| Growth protocol |
Lung cancer cells were grown in RPMI with 10% FBS, 370C incubator, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) with the GeneChip 3’ IVT plus kit (Affymetrix, PN 902416).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 μg of cRNA were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix). Each array was washed and stained with streptavidin–phycoerythrin and amplified with biotinylated anti-streptavidin antibody on the GeneChip Fluidics Station 450 (Affymetrix)
|
| Scan protocol |
Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities.
|
| Description |
20_sh7.BRD.MUT.CEL
Gene expression data from isogenic stable cell lines
|
| Data processing |
The expression data generated were processed using Affy and LIMMA Bioconductor packages using the R-programming environment.
The gene expression profiles were normalized using the RMA algorithm
|
| |
|
| Submission date |
May 20, 2015 |
| Last update date |
Jul 21, 2015 |
| Contact name |
Parantu Shah |
| E-mail(s) |
parantu.shah@gmail.com
|
| Organization name |
The UT MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
7137922121 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE69088 |
Gene expression profiling on isogenic lines expressing wild-type and mutant forms of SMARCA2 and SMARCA4 |
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