|
| Status |
Public on Jun 01, 2011 |
| Title |
Pulmonary Fibrosis patient 89 |
| Sample type |
RNA |
| |
|
| Source name |
Lung sample from recipient organ
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
disease state: validation set for PH
|
| Treatment protocol |
Fresh frozen lung tissue specimens were obtained from the recipient organs of Pulmonary Fibrosis patients undergoing lung transplantation. Specimens were obtained as soon as the first recipient lung was taken out, snap frozen in liquid nitrogen, and stored at -80ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized from 4 ug of RNA with high capacity cDNA Reverse Transcription kits (Applied Byosystems). cDNA-synthesis was carried out on a PTC-100 Programmable Thermal controller (MJ Research). RNA was qualified by RNA nano chips on an Agilent 2100 Bilanalyzer (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Microarray was performed with Genechip Human Gene 1.0 ST on an Affymetrix Genechip Scanner 3000 and Genechip Fluidics Station 450
|
| Description |
Gene expression data from PF patient, validation set
|
| Data processing |
Affymetrix CEL files were imported into Partek software (Partek) and probe-level data were pre-processed. This included robust multi-array average (Rma) background correction and data normalization, which was performed across all arrays using quantile normalization. Background-adjusted, normalized values were then compiled, or summarized, using the median polish technique, to generate a single measure of expression. As an exploratory data analysis, Principal Component Analysis (PCA) mapping and F Ratio analysis (signal-to-noise ratio) were also performed.
|
| |
|
| Submission date |
Oct 28, 2010 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Marco Mura |
| E-mail(s) |
[email protected]
|
| Fax |
4163403602
|
| Organization name |
Toronto Lung Transplant Program
|
| Department |
Medicine/Surgery
|
| Lab |
Latner Thoracic Surgery Research Laboratories
|
| Street address |
585 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2N2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE24988 |
Gene expression profiles based on Pulmonary Artery Pressures in Pulmonary Fibrosis |
|
