|
Status |
Public on Jul 28, 2024 |
Title |
patient C4P4, before apheresis, T cells |
Sample type |
RNA |
|
|
Source name |
T helper cells from the peripheral blood
|
Organism |
Homo sapiens |
Characteristics |
patient id: C4P4 time point: before cell population: CD4+ T cells purity (%): 99.2 rna integrity number: 8.6 age (years): 54 Sex: female study center: Rostock current smoker: yes body mass index: 21.2 course of disease: CIS/RRMS disease duration (years): 0 comorbidities: yes relapses in the past 2 years: 2 edss score: 3.5 relapse presentation: polysymptomatic symptomatic phenotype: new relapse therapy: plasma exchange relapse therapy phase: escalation number of apheresis sessions: 8 clinical evaluation: 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.
|
|
|
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 |
|