|
| Status |
Public on Aug 11, 2011 |
| Title |
ILD Study Number 1111 |
| Sample type |
RNA |
| |
|
| Source name |
Human peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
age_years: 66
sex: F
ethnicity: White
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Model 3000 scanner.
|
| Description |
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
| Data processing |
The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
|
| |
|
| Submission date |
Dec 03, 2009 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Prescott Gurney Woodruff |
| E-mail(s) |
prescott.woodruff@ucsf.edu
|
| Phone |
4155142061
|
| Fax |
4154765712
|
| Organization name |
UCSF
|
| Department |
Medicine
|
| Lab |
Woodruff Lab
|
| Street address |
505 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE19314 |
Sarcoidosis-specific markers from whole blood gene expression |
|
| Relations |
| Reanalyzed by |
GSE122511 |
