|
| Status |
Public on Jul 28, 2024 |
| Title |
patient C2P9, after apheresis, T cells |
| Sample type |
RNA |
| |
|
| Source name |
T helper cells from the peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: C2P9
time point: after
cell population: CD4+ T cells
purity (%): 98.8
rna integrity number: 8.8
age (years): 43
Sex: male
study center: Greifswald
current smoker: no
body mass index: 36.6
course of disease: CIS/RRMS
disease duration (years): 21
comorbidities: yes
relapses in the past 2 years: 2
edss score: 2.5
relapse presentation: monosymptomatic
symptomatic phenotype: new
relapse therapy: plasma exchange
relapse therapy phase: NA
number of apheresis sessions: 5
clinical evaluation: non-responder
|
| Treatment protocol |
The patients were treated according to the approved labels and the guidelines and recommendations of the German Society of Neurology.
|
| Growth protocol |
Up to ~30 ml of peripheral blood were taken from MS patients in relapse immediately before and after therapeutic apheresis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The blood was collected in BD Vacutainer Glass Cell Preparation Tubes (Fisher Scientific). The tubes were centrifuged for the isolation of peripheral blood mononuclear cells (PBMC). B cells were positively selected from the PBMC using CD19 MicroBeads. T helper cells were obtained from the negative fraction of the B-cell separation by first removing non-T cells using the Pan T Cell Isolation Kit (Miltenyi Biotec) and then isolating CD4+ T cells using CD4 MicroBeads (Miltenyi Biotec). The RNA was isolated using the miRNeasy Mini Kit and 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.
|
| Scan protocol |
The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data for a patient with MS who underwent apheresis treatment
|
| 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 4.0.3 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background reduction, intensity normalization, probe set summarization and log2 transformation. The TAC software was also utilized for the analysis of differential alternative splicing. Exon-level processed data are available on the Series record.
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| |
|
| Submission date |
Jul 24, 2024 |
| Last update date |
Jul 29, 2024 |
| 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) |
| GSE272973 |
Transcriptome data of B cells and T helper cells from patients with multiple sclerosis receiving therapeutic apheresis for the treatment of an acute relapse |
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