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Sample GSM6165221 Query DataSets for GSM6165221
Status Public on May 15, 2024
Title PHC [13363PDC212]
Sample type RNA
 
Source name PBMC from PHC
Organism Homo sapiens
Characteristics gender: Female
age (years): 12
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 PHC 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.
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
 
Submission date May 18, 2022
Last update date May 15, 2024
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 GPL571
Series (1)
GSE203241 Age-related blood transcriptional regulators affect disease progression in pediatric multiple sclerosis

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
1007_s_at 0.639087
1053_at 0.459663
117_at 0.458515
121_at 0.436872
1255_g_at -0.180462
1294_at 1.10515
1316_at 0.255118
1320_at -0.1862
1405_i_at 2.61087
1431_at -0.102599
1438_at -0.11648
1487_at 0.760746
1494_f_at -0.0984468
1598_g_at 0.298939
160020_at 0.547197
1729_at 1.27165
177_at -0.0839358
1773_at 0.0343249
179_at 0.407945
1861_at 0.0519161

Total number of rows: 22277

Table truncated, full table size 438 Kbytes.




Supplementary file Size Download File type/resource
GSM6165221_13363PDC212.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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