|
| Status |
Public on Nov 23, 2015 |
| Title |
Moderate Risk_054-00590 |
| Sample type |
RNA |
| |
|
| Source name |
Moderate Risk_whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype/group: Moderate Risk
tissue: whole blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole blood drawn into PAXgene tubes using the PAXgene Blood RNA kit (PreAnalytiX; Qiagen GmbH-USA). The quality and quantity of the RNA was confirmed using the Nanodrop 1000 Spectrophotomer (Thermo Fisher Scientific, Wilmington, DE) and by RT PCR.
|
| Label |
biotin
|
| Label protocol |
RNA was amplified and the cRNA was biotinylated using the Ambion Illumina TotalPrep RNA Amplification Kit (Life Technologies, Carlsbad, CA).
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
A comprehensive quality control process was performed on all arrays using the lumi package (version 2.6.0) in Bioconductor in the R environment (version 2.14.0) for statistical computing. Quality of the raw data was assessed using the percent of probes present, MA plots, boxplots of the expression distribution, and heatmaps to visualize the correlation between samples. Samples in which the percent of probes present was 15% or less were excluded. The lumi package was used to make background corrections, log-transform expression values, and carry out quantile normalization.
|
| |
|
| Submission date |
Jun 17, 2013 |
| Last update date |
Nov 23, 2015 |
| Contact name |
Deborah A Lewis |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University Medical Center
|
| Street address |
201 Trent Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE48000 |
Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism [Set1] |
|
