|
| Status |
Public on Sep 21, 2010 |
| Title |
baseline_45familylinkage_GM12878_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Lymphoblastoid cell lines derived from GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
coriell cell line repository identifier: GM12878
cell type: lymphoblastoid
|
| Biomaterial provider |
Coriell Cell Repositories
|
| 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 were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human HG-Focus Target Array (U95v2). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM12878.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Jun 24, 2009 |
| Last update date |
Sep 21, 2010 |
| Contact name |
Renuka Nayak |
| Organization name |
HHMI, University of Pennsylvania
|
| Street address |
3516 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL201 |
| Series (1) |
| GSE16778 |
Gene expression levels in immortalized B cells from members of 45 CEPH-Utah pedigrees |
|
