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Sample GSM1525435 Query DataSets for GSM1525435
Status Public on Feb 17, 2015
Title Human_fibroblast_P1
Sample type RNA
 
Source name patient 1
Organism Homo sapiens
Characteristics disease state: schizophrenia
tissue: skin
cell type: fibroblast
gender: Male
age: 55
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 4.15843075
7892502 2.9598207
7892503 2.23325729
7892504 7.408748235
7892505 1.878381705
7892506 3.046299662
7892507 3.159043044
7892508 3.416755385
7892509 9.260781752
7892510 3.629751027
7892511 2.387654509
7892512 4.819138832
7892513 1.932714673
7892514 9.109462309
7892515 7.676173222
7892516 2.732593086
7892517 2.6600678
7892518 2.330332876
7892519 4.201986754
7892520 7.607882369

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1525435_P1.cel.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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