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Sample GSM4213547 Query DataSets for GSM4213547
Status Public on Dec 11, 2020
Title P/MS [568RMS]
Sample type RNA
 
Source name PBMC from P/MS
Organism Homo sapiens
Characteristics gender: Male
age (years): 39.67
Treatment protocol PBMC were purified from Ficoll hypaque gradient (Invitrogen, USA)
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description PBMC gene expression from P/MS patients
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
The Supplementary Tables 1-3 included statistically significant genes obtained by comparison of each experimental group Multiple Sclerosis only (MSO), Psoriasis only (PSO), Psoriasis and Multiple Sclerosis comorbid patients (P/MS) with Healthy Controls (HC) The Supplementary Table 4 include upstream regulators for PSO related genes.
Supplementary Table 1 - "MSO Vs HC"
Supplementary Table 2 - "PSO Vs HC"
Supplementary Table 3 - "P/MS Vs HC"
Supplementary Table 4 - "Upstream regulators for PSO genes"
 
Submission date Dec 11, 2019
Last update date Dec 12, 2020
Contact name Michael Gurevich
E-mail(s) Michael.Gurevich@sheba.health.gov.il
Organization name Sheba Medical Center
Department Multiple Sclerosis Center
Lab Neurogenomics and Neuroimmunology
Street address Tel Hashomer
City Ramat Gan
ZIP/Postal code 52621
Country Israel
 
Platform ID GPL96
Series (1)
GSE141804 Co-Morbid Multiple Sclerosis and Psoriasis: Clinical Outcomes and Gene Expression

Data table header descriptions
ID_REF
VALUE Following scanning of the arrays, the microarray raw data were initially normalized by R Bioconductor Packages, all arrays were normalized serially using a single sample microarray normalization approach designed for personal medicine workflows (SCAN Normalization). An empirical Bayes approach (ComBat algorithm) was used to minimize the batch effect in the data

Data table
ID_REF VALUE
1007_s_at 0.425952
1053_at 0.309719
117_at 0.744529
121_at 0.477313
1255_g_at -0.208862
1294_at 1.10709
1316_at 0.189515
1320_at -0.182844
1405_i_at 2.81079
1431_at -0.193225
1438_at -0.18503
1487_at 0.695427
1494_f_at -0.132623
1598_g_at 0.363687
160020_at 0.602147
1729_at 1.10269
177_at -0.0758969
1773_at -0.0496889
179_at 0.513597
1861_at -0.117843

Total number of rows: 22215

Table truncated, full table size 437 Kbytes.




Supplementary file Size Download File type/resource
GSM4213547_568RMS.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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