|
| Status |
Public on May 11, 2009 |
| Title |
PBMC Exposed, biological rep 3 (HG-U133A) |
| Sample type |
RNA |
| |
|
| Source name |
PBMC Exposed
|
| Organism |
Homo sapiens |
| Characteristics |
Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood was collected from each subject at the beginning of the workday around 0900 hr and processed within 6 hr of collection. PBMC were isolated by Ficoll-Paque and lysed in RLT buffer (Qiagen). Lysates were frozen at -80°C and later thawed and extracted using Qiagen's RNeasy mini kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared according to the GeneChip Eukaryotic Small Sample Target Labeling Assay Version II (Affymetrix 2003a), with the exception that the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) was used instead of ethanol precipitation. Total RNA (100 ng) was amplified for each sample, with 400 ng of first-round cRNA used for the second round of cDNA synthesis.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133A and B chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner GA 2500.
|
| Description |
biotin
|
| Data processing |
RMA (robust multi-chip averaging) from the Bioconductor Affymetrix package was used for quantile normalization and background adjustment.
|
| |
|
| Submission date |
Nov 20, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Cliona McHale |
| E-mail(s) |
[email protected]
|
| Phone |
510-6435100
|
| Organization name |
University of California Berkeley
|
| Department |
School of Public Health
|
| Lab |
Smith
|
| Street address |
384 Li Ka Shing Center
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3370 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE9569 |
Gene expression in benzene-exposed workers |
|
