|
| Status |
Public on Aug 04, 2011 |
| Title |
GM12878-0hr |
| Sample type |
RNA |
| |
|
| Source name |
Lymphoblastoid cell line, 0hr
|
| Organism |
Homo sapiens |
| Characteristics |
coriell cell line: GM12878
cell type: lymphoblastoid cells
ceph id: 1463.2
relationship: mother
treatment: none
treatment time: 0hr
|
| Biomaterial provider |
Corriell Cell Repositories; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878
|
| Treatment protocol |
10 Gy of ionizing radiation (IR) in a 137Cs irradiator.
|
| Growth protocol |
The cells were grown at a density of 500,000 cells/ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini-Kit (Qiagen) as per the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion/Applied Biosystems) from 1 microg of total RNA following manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human U133A 2.0 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Baseline, GM12878
Gene expression data from lymphoblastoid cells prior to irradiation.
|
| Data processing |
The data were analyzed with Expression Console software using the MAS5 probe summary method and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Jan 24, 2011 |
| Last update date |
Sep 19, 2011 |
| Contact name |
Michael Patrick Morley |
| E-mail(s) |
[email protected]
|
| Phone |
215-898-2026
|
| Organization name |
Perelman School of Medicine at the University of Pennsylvania
|
| Department |
Penn Cardiovascular Institute
|
| Street address |
3400 Civic Center Blvd, Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE26835 |
Genetic variation in radiation-induced cell death |
|
