|
| Status |
Public on Feb 17, 2015 |
| Title |
Human_fibroblast_P4 |
| Sample type |
RNA |
| |
|
| Source name |
patient 4
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: schizophrenia
tissue: skin
cell type: fibroblast
gender: Male
age: 36
|
| 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 |
|
