|
| Status |
Public on Feb 26, 2014 |
| Title |
leukocyte I699JJ |
| Sample type |
RNA |
| |
|
| Source name |
whole blood leukocytes
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
group: juvenile idiopathic arthritis patient
month of visit: 0
patient id: 13080
|
| Treatment protocol |
2.5 ml of blood was collected in a PAXgene tube (PreAnalytiX GmbH, Hilden, Germany). Samples were stored at -80 C prior to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from whole blood PAXgene specimens using a PAXgene Blood RNA kit (Qiagen,Valencia, CA) as recommended by the manufacturer, including a DNAse (Qiagen) step to remove genomic DNA. Globin transcripts were reduced using GLOBINclear-Human (Ambion , Austin, TX ).
|
| Label |
Cy3
|
| Label protocol |
cRNA was produced from reverse transcribed cDNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to Illumina WG-6 v3 or Illumina HT-12 v4 human whole genome microarrays, and stained according to the manufacturer’s directions.
|
| Scan protocol |
Scanning was performed using Illumina's iScan scanner
|
| Data processing |
Because of microarray product changes in the course of the study, raw data were reduced to contain 39426 common probes between the microarrays. Data in Matrix (raw) table contain values from Illumina's Genome Studio software and detection p-values above background. Sample tables contain variance stabilized and robust spline values from the lumi package. Batch effects were removed using the ComBat algorithm in the sva package.
|
| |
|
| Submission date |
Feb 25, 2014 |
| Last update date |
Feb 26, 2014 |
| Contact name |
Bart Frank |
| E-mail(s) |
[email protected]
|
| Organization name |
OMRF
|
| Street address |
825 NE 13 St
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73103 |
| Country |
USA |
| |
|
| Platform ID |
GPL6884 |
| Series (1) |
| GSE55319 |
Whole Blood Gene Expression Profiling Predicts Therapeutic Response in Polyarticular Juvenile Idiopathic Arthritis at 4 Months |
|
