|
| Status |
Public on Jun 21, 2013 |
| Title |
LT101536 |
| Sample type |
RNA |
| |
|
| Source name |
Lung tissue
|
| Organism |
Homo sapiens |
| Characteristics |
age: 57
gender: Male
final diagnosis: IPF/UIP
repository: LTRC
tissue source: L Lower
preservative: RNAlater
rin: 8.4
smoking status: former
quit how many years ago: --
pack years: 40
st. george's total score: 82.92
fvc pre-bronchodilator % predicted: 59.2824
dlco % predicted: 32.7506
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including small RNA species was isolated from approximately 100 mg of snap-frozen lung tissue using the mirVana kit (AB/Ambion, Austin TX).
|
| Label |
biotin
|
| Label protocol |
mRNA microarray target labeling was conducted using 300 ng of total RNA and the Message Amp II kit.
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Data processing |
Intensity data were log2-transformed, quantile normalized using RMA, and expression levels were summarized on a transcript level using the mean value of all probesets mapping to a transcript. Non-expressed and invariant transcripts were removed using a median variance filter, corrected by a Benjamini-Hochberg false discovery rate (FDR) of 0.10, resulting in a final dataset of 11950 transcript measurements across 217 samples
|
| |
|
| Submission date |
Oct 01, 2011 |
| Last update date |
Sep 23, 2014 |
| Contact name |
David Schwartz |
| E-mail(s) |
DAVID.SCHWARTZ@ucdenver.edu
|
| Phone |
303-724-1783
|
| Organization name |
University of Colorado, Anschutz Medical Campus
|
| Department |
Medicine
|
| Street address |
Anschutz Medical Campus
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE32537 |
Molecular phenotyping of the idiopathic interstitial pneumonias [mRNA] |
| GSE32539 |
Molecular phenotyping of the idiopathic interstitial pneumonias identifies two Subtypes of idiopathic pulmonary fibrosis. |
|
