|
| Status |
Public on Mar 05, 2010 |
| Title |
SAMPLE 43 PBMC |
| Sample type |
RNA |
| |
|
| Source name |
PBMC_Wegener's granulomatosis
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
wg signature status: WG Sig +
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Venous blood was collected by simple venipuncture under aseptic conditions. All samples were processed within one hour of collection to minimize gene expression variations associated with longer sample incubation times. PBMCs were separated by Ficoll density gradient, and PMNs isolated following 1-3 rounds of hypotonic RBC lysis. Cells were assessed for viability by trypan blue dye exclusion, were immediately lysed in Trizol reagent (Invitrogen, Carlsbad, California) and stored at -80°C. Total RNA was extracted from either the PBMC or PMN fractions using the Trizol reagent method (Invitrogen, Carlsbad, California). Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA), and the quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to Illumina HumanRef-8 v2 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.
|
| Scan protocol |
All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.
|
| Description |
SAMPLE 43 PBMC
Wegener's granulomatosis biological replicate 20
|
| Data processing |
A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed.
|
| |
|
| Submission date |
Nov 04, 2009 |
| Last update date |
Mar 05, 2010 |
| Contact name |
Alan E. Berger |
| E-mail(s) |
[email protected]
|
| Phone |
301-938-3565
|
| Organization name |
Johns Hopkins University
|
| Department |
School of Medicine
|
| Lab |
Division of Allergy and Clinical Immunology
|
| Street address |
5501 Hopkins Bayview Circle Room 3B.74C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE18885 |
Expression data from human Wegener’s granulomatosis patients and normal controls in PBMCs and in PMNs |
|
