|
| Status |
Public on Jul 15, 2009 |
| Title |
Definite MS_551AV54 |
| Sample type |
RNA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Definite MS
cell type: Peripheral blood mononuclear cells
age: 33
gender: Female
time to next relapse(days): 676
|
| Treatment protocol |
Peripheral blood mononuclear cells (PBMC) were separated on ficoll-hypaque gradient
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA
|
| |
|
| Hybridization protocol |
cDNA was synthesized, labeled, hybridized to either HU-133A or HU133A-2 containing 22,215 gene-transcripts according to Affymetrix (Inc, Santa Clara, CA) protocol
|
| Scan protocol |
Hewlett Packard, GeneArray-TM scanner G2500A
|
| Description |
working set54
|
| Data processing |
Data analysis was performed by Partek Genomics Solution software (www.partek.com ). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. The RMA correction included: 1) values background correction; 2) quantile normalization; 3) log2 transformation; 4) median polish summarization. In order to avoid the noise caused by variable set effects we normalized each set to pre-saved distribution pattern of a well balanced set used as a reference distribution. To reduce batch effect, Analysis of Variance (ANOVA) multiple model analysis was applied. Source of variation was analyzed; non-relevant batches effects such as array type, working batch, patient age and gender were eliminated.
|
| |
|
| Submission date |
Mar 16, 2009 |
| Last update date |
Jul 14, 2009 |
| Contact name |
Michael Gurevich |
| E-mail(s) |
Michael.Gurevich@sheba.health.gov.il
|
| Organization name |
Sheba Medical Center
|
| Department |
Multiple Sclerosis Center
|
| Lab |
Neurogenomics and Neuroimmunology
|
| Street address |
Tel Hashomer
|
| City |
Ramat Gan |
| ZIP/Postal code |
52621 |
| Country |
Israel |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE15245 |
Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells |
|
