|
| Status |
Public on May 15, 2024 |
| Title |
POMS [12832PDMS204] |
| Sample type |
RNA |
| |
|
| Source name |
PBMC from POMS
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age (years): 16
|
| Treatment protocol |
PBMC were purified from Ficoll hypaque gradient (Invitrogen, USA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
PBMC gene expression from POMS patients
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Following scanning of the arrays, the microarray raw data were initially normalized by R Bioconductor Packages, all arrays were normalized serially using a single sample microarray normalization approach designed for personal medicine workflows (SCAN Normalization). An empirical Bayes approach (ComBat algorithm) was used to minimize the batch effect in the data
|
| |
|
| Submission date |
May 18, 2022 |
| Last update date |
May 15, 2024 |
| 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) |
| GSE203241 |
Age-related blood transcriptional regulators affect disease progression in pediatric multiple sclerosis |
|
