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Sample GSM1525449 Query DataSets for GSM1525449
Status Public on Feb 17, 2015
Title Human_fibroblast_P15
Sample type RNA
 
Source name patient 15
Organism Homo sapiens
Characteristics disease state: schizophrenia
tissue: skin
cell type: fibroblast
gender: Female
age: 30
Growth protocol Skin biopsies (3 mm2) were collected under local anaesthesia from the scapular region using aseptic conditions and immediately immersed in a saline solution (PBS). All primary cultures were grown in Eagle’s minimum essential medium supplemented with 10% of foetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 μg/ml), non-essential amino acids (1% v/v) and glutamine (1% v/v) under optimal conditions (37° C, 5% CO2).
Extracted molecule total RNA
Extraction protocol RNA from fibroblasts was extracted using the NucleoSpin kit (MACHEREY-NAGEL, Düren , Germany) according to the manufacturer’s instructions.
Label biotin
Label protocol ssDNA was labelled with biotin according to the standard Affymetrix protocol (GeneAtlasTM WT Expression Kit User Manual)
 
Hybridization protocol Following fragmentation, 5.5 µg of ssDNA were hybridized for 20 hours at 48°C on Human Gene 1.1 ST Array Strip. Array Strips were washed and stained using the GeneAtlas instrument.
Scan protocol Array Strips were scanned using the GeneAtlas instrument.
Description Cell line was cultured until the 5th passage
Data processing Data processing was performed using R/Bioconductor. Oligo package was used to read CEL files and compute the log intensities of gene expression by exploiting Robust Multi-array Average (RMA) algorithm. Linear models fitting (LmFit) and Empirical Bayes method (eBayes) from the BioConductor limma package were used to test the differences in mRNA levels.
 
Submission date Oct 14, 2014
Last update date Feb 18, 2015
Contact name Nadia Cattane
E-mail(s) ncattane@fatebenefratelli.it
Organization name University of Brescia
Department Department of Translational and Molecular Medicine
Street address Viale Europa 11
City Brescia
State/province BS
ZIP/Postal code 25123
Country Italy
 
Platform ID GPL11532
Series (1)
GSE62333 Transcriptomic profiles of skin fibroblasts from patients affected by schizophrenia and controls

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
7892501 2.547362828
7892502 3.123430461
7892503 1.704356792
7892504 7.016305471
7892505 2.747176814
7892506 3.77726446
7892507 3.366150159
7892508 4.918960567
7892509 9.144428624
7892510 3.796498152
7892511 3.260786897
7892512 3.888644273
7892513 2.363549532
7892514 10.29459969
7892515 8.44577799
7892516 2.023070818
7892517 2.520229556
7892518 2.830016272
7892519 3.773885118
7892520 8.276539359

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1525449_P15.cel.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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