|
| Status |
Public on Aug 31, 2017 |
| Title |
control_ IR_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MCF7 control line, IR
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: p53beta wild type
treatment: 4hr post 20gy irradiation
|
| Treatment protocol |
Cells are ubjected to 20gy ionizing irradiation using X ray irradiator-X-Ray 160 (Precision X ray inc)
|
| Growth protocol |
p53β CRISPR and control cells are maintained in DMEM supplemented with 10% fetal culf serum and 1% antibiotics and grow at 37 centigree
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from approximate 1 million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. All samples were treated with DNAse I (Life technology) to remove trace amounts of genomic DNA.
|
| Label |
biotin
|
| Label protocol |
Samples were labeled using the Affymetrix GeneChip WT Plus Reagent kit according to the protocol provided by Affymetrix.
|
| |
|
| Hybridization protocol |
Samples were hybridized to the Affymetrix GeneChip Human Transcriptome Array 2.0 according to protocols provided by Affymetrix.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
Processed by Affymetrix TAC 3.0
|
| Data processing |
Raw data were processed with the Expression Console Build 1.4.1.46 Workflow for HTA-2_0 (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with the Transcriptome Analysis Console 3.0 for Alternative Splicing Analysis. http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets.
RMA
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
Aug 31, 2017 |
| Contact name |
Michael Barry Kastan |
| E-mail(s) |
michael.kastan@duke.edu
|
| Organization name |
Duke University
|
| Department |
Duke Cancer Institute
|
| Street address |
2424 Erwin Road
|
| City |
Durham |
| State/province |
NORTH CAROLINA |
| ZIP/Postal code |
27705 |
| Country |
USA |
| |
|
| Platform ID |
GPL17585 |
| Series (1) |
| GSE84813 |
Exon level expression profile of MCF7 cells with p53β splice variant knocked out 4hr post 20gy irradiation |
|
