|
| Status |
Public on Mar 01, 2011 |
| Title |
PBMC_ectopic_validation_16 |
| Sample type |
RNA |
| |
|
| Source name |
PBMCs from patients with other cancer types (e.g., gastrointestinal and brain cancers)
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: Ectopic
tissue: peripheral blood leukocytes
data set: validation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from peripheral blood mononuclear cells was isolated using the Ambion Ribopure™-Blood kit (Ambion, Austin, TX).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix IVT 1-cycle protocol from 2.5 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15ug of labeled cRNA were hybridized on HU133 Plus 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.
|
| Scan protocol |
GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).
|
| Description |
Blood collection: Samples collected by leukapheresis and stored in liquid nitrogen.
PBMC isolation:
|
| Data processing |
Data processing was performed in a pilot revision control system entitled Quality-Auditable Data Repository and Analysis (QUADRA). For fully versioned and annotated source code and data objects, please see http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project.
Data were RMA normalized according to the source code found at http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project/human-dataprep.
|
| |
|
| Submission date |
Feb 28, 2011 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Erich Huang |
| E-mail(s) |
[email protected]
|
| Phone |
919-684-6849
|
| Fax |
919-681-8973
|
| Organization name |
Duke University
|
| Department |
Institute for Genome Sciences and Policy
|
| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE27562 |
Expression data from human PBMCs from breast cancer patients and controls |
| GSE27567 |
Integrating Factor Analysis and a Transgenic Mouse Model to Reveal a Peripheral Blood Predictor of Breast Tumors |
|
| Relations |
| Reanalyzed by |
GSE122511 |
