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Sample GSM1888116 Query DataSets for GSM1888116
Status Public on Sep 19, 2015
Title Patient 3, CD8+ cells, before second dose of fingolimod [exon-level]
Sample type RNA
 
Source name Peripheral blood CD8+ cells
Organism Homo sapiens
Characteristics patient identifier: WKSB-4693
gender: female
age in years at baseline: 43
disease duration in years at baseline: 1
previous treatment: interferon-beta-1a intramuscular
treatment gap in months: 1
edss at baseline: 4.0
edss after 1 year: 3.5
edss after 2 years: 3.5
edss after 3 years: 3.5
edss after 4 years: 6.0
relapses during the year prior to fingolimod: 2
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: 3
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 CD8+ cells were separated by magnetic-activated cell sorting using Whole Blood CD8 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 200 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 18, 2015
Last update date Mar 23, 2018
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 GPL17585
Series (2)
GSE73172 Transcriptome data of multiple sclerosis patients receiving fingolimod therapy [HTA-2_0, CD8+ cells, exon level]
GSE73174 Transcriptome data of multiple sclerosis patients receiving fingolimod therapy
Relations
Alternative to GSM1885020 (gene-level analysis)

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
JUC01000001.hg.1 5.44698
JUC01000002.hg.1 4.163072
JUC01000003.hg.1 5.803759
JUC01000004.hg.1 6.11376
JUC01000005.hg.1 6.952794
JUC01000006.hg.1 6.517836
JUC01000007.hg.1 3.304406
JUC01000008.hg.1 5.054455
JUC01000009.hg.1 2.202871
JUC01000010.hg.1 1.588883
JUC01000011.hg.1 10.81146
JUC01000012.hg.1 7.536605
JUC01000013.hg.1 10.24702
JUC01000014.hg.1 8.6388
JUC01000015.hg.1 5.206074
JUC01000016.hg.1 7.367907
JUC01000017.hg.1 5.554861
JUC01000018.hg.1 7.037335
JUC01000019.hg.1 7.459346
JUC01000020.hg.1 7.459346

Total number of rows: 914585

Table truncated, full table size 23435 Kbytes.




Supplementary file Size Download File type/resource
GSM1888116_CD8_Pat03_24_hours.CEL.gz 22.0 Mb (ftp)(http) CEL
GSM1888116_CD8_Pat03_24_hours.rma-alt-splice-dabg.chp.gz 9.3 Mb (ftp)(http) CHP
Processed data included within Sample table

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