|
| Status |
Public on Sep 19, 2015 |
| Title |
Patient 3, CD4+ cells, before second dose of fingolimod [exon-level] |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood CD4+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient identifier: YHCG-2832
gender: female
age in years at baseline: 29
disease duration in years at baseline: 5
previous treatment: glatiramer acetate
treatment gap in months: <1
edss at baseline: 2.5
edss after 1 year: 1.5
edss after 2 years: 1.5
edss after 3 years: 1.5
edss after 4 years: 1.5
relapses during the year prior to fingolimod: 3
relapses during 1-year follow-up: 0
relapses during 2-year follow-up: 0
relapses during 3-year follow-up: 0
relapses during 4-year follow-up: 0
completed years of fingolimod therapy: >=4
|
| Treatment protocol |
Patients were treated with fingolimod (Gilenya, Novartis) according to the approved label (0.5 mg orally once-daily) and the guidelines and recommendations of the German Society of Neurology.
|
| Growth protocol |
Patient blood samples were taken immediately before the first dose of fingolimod as well as one day and three months post therapy initiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood CD4+ cells were separated by magnetic-activated cell sorting using Whole Blood CD4 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.
|
| Label |
Biotin
|
| Label protocol |
According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 70 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.
|
| |
|
| Hybridization protocol |
Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.
|
| Scan protocol |
The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data from a multiple sclerosis patient treated with fingolimod
|
| Data processing |
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console (AGCC) software version 4.0. The data were then processed using Expression Console version 1.3.1. The robust multi-array average (RMA) algorithm was applied with the default configuration, which includes a log2 data transformation and quantile normalization. In this step, the measured signal intensities of >6 million probes were summarized into gene level probe sets (n=70523) and exon level probe sets (n=914585). The Transcriptome Analysis Console (TAC) software version 1.0 was utilized to analyze the RNA expression dynamics.
|
| |
|
| Submission date |
Sep 16, 2015 |
| Last update date |
Mar 23, 2018 |
| Contact name |
Michael Hecker |
| E-mail(s) |
michael.hecker@rocketmail.com
|
| Organization name |
University of Rostock
|
| Department |
Department of Neurology
|
| Lab |
Division of Neuroimmunology
|
| Street address |
Gehlsheimer Str. 20
|
| City |
Rostock |
| ZIP/Postal code |
18147 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17585 |
| Series (2) |
| GSE73080 |
Transcriptome data of multiple sclerosis patients receiving fingolimod therapy [HTA-2_0, CD4+ cells, exon level] |
| GSE73174 |
Transcriptome data of multiple sclerosis patients receiving fingolimod therapy |
|
| Relations |
| Alternative to |
GSM1884960 (gene-level analysis) |
