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Sample GSM1885001 Query DataSets for GSM1885001
Status Public on Sep 19, 2015
Title Patient 7, CD4+ cells, before first dose of fingolimod [exon-level]
Sample type RNA
Source name Peripheral blood CD4+ cells
Organism Homo sapiens
Characteristics patient identifier: DMPU-9668
gender: female
age in years at baseline: 46
disease duration in years at baseline: 9
previous treatment: interferon-beta-1b subcutaneous
treatment gap in months: <1
edss at baseline: 4.0
edss after 1 year: 4.0
edss after 2 years: 4.0
edss after 3 years: 4.0
edss after 4 years: 4.0
relapses during the year prior to fingolimod: 1
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 May 24, 2018
Contact name Michael Hecker
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
Alternative to GSM1884971 (gene-level analysis)

Data table header descriptions
VALUE RMA signal intensity

Data table
JUC01000001.hg.1 5.194702
JUC01000002.hg.1 4.122219
JUC01000003.hg.1 6.208089
JUC01000004.hg.1 6.015738
JUC01000005.hg.1 6.496063
JUC01000006.hg.1 6.174938
JUC01000007.hg.1 3.929366
JUC01000008.hg.1 5.128558
JUC01000009.hg.1 2.161441
JUC01000010.hg.1 2.24581
JUC01000011.hg.1 10.86348
JUC01000012.hg.1 7.774268
JUC01000013.hg.1 10.04229
JUC01000014.hg.1 8.530106
JUC01000015.hg.1 5.458814
JUC01000016.hg.1 7.075453
JUC01000017.hg.1 6.256594
JUC01000018.hg.1 8.064842
JUC01000019.hg.1 6.764317
JUC01000020.hg.1 6.764317

Total number of rows: 914585

Table truncated, full table size 23452 Kbytes.

Supplementary file Size Download File type/resource
GSM1885001_CD4_Pat07_baseline.CEL.gz 21.1 Mb (ftp)(http) CEL
GSM1885001_CD4_Pat07_baseline.rma-alt-splice-dabg.chp.gz 9.3 Mb (ftp)(http) CHP
Processed data included within Sample table

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