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Sample GSM3262495 Query DataSets for GSM3262495
Status Public on Sep 29, 2020
Title blood_treated_P71
Sample type RNA
 
Source name whole blood, patient 71, after 14 days treatment
Organism Homo sapiens
Characteristics disease status: relapse remitting multiple sclerosis (MS)
tissue: whole blood
treatment: short chain fatty acid propionate (PA)
time point: 14 days
sample_pair: 71
sample type: treatment
Treatment protocol Peripheral blood was drawn in PaxGene tubes (BD) at baseline and after 14 days of treatment. Blood tubes were gently inverted multiple times and allowed to rest for two hours to ensure RNA stability. Samples were frozen on -80°C for subsequent RNA purification.
Growth protocol Relapse remitting MS patients were recruited at the St. Josef Hospital Bochum following inclusion and exclusion criteria of ethic approval from the Ruhr-University Bochum.
Extracted molecule total RNA
Extraction protocol Trizol extraction of whole RNA was performed after manufacturer's instructions.
Label biotin
Label protocol Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA). In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.
 
Hybridization protocol 3.8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640.
Scan protocol Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.
Description P190_08_71-2
Data processing Data processing was performed using BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team.
 
Submission date Jul 09, 2018
Last update date Sep 29, 2020
Contact name Ori Staszewski
E-mail(s) ori.staszewski@uniklinik-freiburg.de
Organization name University Medical Center Freiburg
Department Institute of Neuropathology
Street address Breisacher Str. 64
City Freiburg
ZIP/Postal code D-79106
Country Germany
 
Platform ID GPL23159
Series (1)
GSE116835 Expression data from human whole blood of propionate treated MS patients

Data table header descriptions
ID_REF
VALUE Log2 GC-RMA

Data table
ID_REF VALUE
23064070 7.839888573
23064071 6.100893974
23064072 5.29257822
23064073 6.792260647
23064074 3.687768698
23064075 8.046956062
23064076 4.00681591
23064077 7.014712811
23064078 7.601097107
23064079 4.580024242
23064080 12.31568146
23064081 3.880740643
23064083 4.016136169
23064084 2.391023874
23064085 4.809920788
23064086 3.679701805
23064087 5.519147873
23064088 5.620757103
23064089 2.784592152
23064090 5.297587395

Total number of rows: 27189

Table truncated, full table size 792 Kbytes.




Supplementary file Size Download File type/resource
GSM3262495_P190_08_71-2.CEL.gz 1.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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