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Sample GSM1525425 Query DataSets for GSM1525425
Status Public on Feb 17, 2015
Title Human_fibroblast_C11
Sample type RNA
 
Source name control 11
Organism Homo sapiens
Characteristics disease state: control
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 4.973119087
7892502 3.408520999
7892503 2.077983008
7892504 7.258673438
7892505 2.301813106
7892506 2.996300523
7892507 2.494442473
7892508 3.686463357
7892509 10.11858653
7892510 3.607563775
7892511 2.531980384
7892512 3.64207933
7892513 1.947377061
7892514 10.38513211
7892515 7.762350143
7892516 4.351849797
7892517 3.40945032
7892518 3.648108645
7892519 3.420725349
7892520 6.863461484

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1525425_C11.cel.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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