|
| Status |
Public on Dec 14, 2021 |
| Title |
sample 54, RRMS - natalizumab 13 |
| Sample type |
RNA |
| |
|
| Source name |
B cells from the peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
subject identifier: TK64I
group: RRMS patient
therapy: natalizumab
Sex: female
age (years): 40
disease duration (years): 17.1
edss score: 7.5
relapses in previous year: 0
|
| Treatment protocol |
The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.
|
| Growth protocol |
Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 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 Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.
|
| Scan protocol |
The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data for a patient with RRMS treated with natalizumab
|
| Data processing |
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.
|
| |
|
| Submission date |
Dec 13, 2021 |
| Last update date |
Dec 14, 2021 |
| 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 |
GPL23126 |
| Series (1) |
| GSE190847 |
Transcriptome data of B cells from patients with multiple sclerosis and healthy controls |
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