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Sample GSM5732884 Query DataSets for GSM5732884
Status Public on Dec 14, 2021
Title sample 33, PPMS 5
Sample type RNA
 
Source name B cells from the peripheral blood
Organism Homo sapiens
Characteristics subject identifier: GD25M
group: PPMS patient
therapy: glucocorticosteroids
Sex: male
age (years): 57
disease duration (years): 5.1
edss score: 3.5
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 PPMS
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 Jul 14, 2023
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

Data table header descriptions
ID_REF
VALUE Gene-level SST-RMA signal intensity

Data table
ID_REF VALUE
TC0100006432.hg.1 3.64975
TC0100006433.hg.1 3.07001
TC0100006434.hg.1 3.51226
TC0100006435.hg.1 3.20385
TC0100006436.hg.1 3.26326
TC0100006437.hg.1 2.98847
TC0100006438.hg.1 7.41219
TC0100006439.hg.1 5.44508
TC0100006440.hg.1 3.56124
TC0100006441.hg.1 5.46854
TC0100006442.hg.1 3.23212
TC0100006443.hg.1 3.92533
TC0100006444.hg.1 2.9821
TC0100006445.hg.1 3.81051
TC0100006446.hg.1 3.50152
TC0100006447.hg.1 18.7575
TC0100006448.hg.1 3.21743
TC0100006449.hg.1 3.07323
TC0100006450.hg.1 3.22354
TC0100006451.hg.1 4.4452

Total number of rows: 135750

Table truncated, full table size 3449 Kbytes.




Supplementary file Size Download File type/resource
GSM5732884_sample_33_PPMS_5.CEL.gz 21.2 Mb (ftp)(http) CEL
GSM5732884_sample_33_PPMS_5.sst-rma-combined-dabg.chp.gz 17.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data are available on Series record

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