|
| Status |
Public on Apr 16, 2010 |
| Title |
carpal-tunnel derived fibroblasts 4 Codelink |
| Sample type |
RNA |
| |
|
| Source name |
Fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblasts
disease status: carpal-tunnel
|
| Treatment protocol |
Once the cells reached 80% confluence RNA was extracted
|
| Growth protocol |
Fibroblasts from both carpal tunnel and Dupuytren's contracture were grown to confluenced
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNA isolation kit from Qiagen.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified, labeled and hybridized according to the manufacturers' protocols. Biotin labeled cRNA probe was prepared by a linear amplification method. After first and second strand synthesis, the cDNA served as the template for an in vitro transcription (IVT) reaction to produce the target cRNA.
|
| |
|
| Hybridization protocol |
The biotin labeled cRNA (10 μg) was hybridized overnight in a temperature controlled shaking incubator at 37°C.
|
| Scan protocol |
Post-hybridization processing included a stringent wash to remove unbound and non-specifically hybridized target molecules, a staining step with a Cy™5-streptavidin conjugate followed by several non-stringent washing steps to remove unbound conjugate. Following a final rinse, the bioarrays were dried by centrifugation and scanned. The CodeLink bioarrays were read in a Lumonix-Packard scanner.
|
| Data processing |
Data were median-normalized using CodeLink software (available as a supplementary file on the Series record). Further normalization was performed using MS Excel via median array normalization (provided in Sample data table below). The median normalized data for each individual array was obtained by dividing each probe intensity value by the median value of that entire array. Significance determination was performed using the Significance Analysis of Microarrays (SAM) software package.
|
| |
|
| Submission date |
Apr 08, 2010 |
| Last update date |
Apr 15, 2010 |
| Contact name |
Latha Satish |
| E-mail(s) |
lsatish@wpahs.org
|
| Phone |
412-359-6594
|
| Organization name |
Allegheny-Singer Research Institute
|
| Department |
Center for Genomic Sciences
|
| Street address |
320 E North Avenue
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15212 |
| Country |
USA |
| |
|
| Platform ID |
GPL10301 |
| Series (1) |
| GSE21221 |
Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture |
|
