|
| Status |
Public on Sep 11, 2012 |
| Title |
6967-08-COPD |
| Sample type |
RNA |
| |
|
| Source name |
Whole lung tissue
|
| Organism |
Homo sapiens |
| Characteristics |
lm: 354.3304218
patient: 6967
slice: 8
copd status: 1
Sex: Female
age: 61
pack years: 25
notes: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
High molecular weight RNA was isolated from tissue cores using the miRNeasy Mini Kit (Qiagen). The RNA integrity was assessed using an Agilent 2100 Bioanalyzer and RNA purity was assessed using a NanoDrop spectrophotometer. One ug of RNA was processed and used as starting material for the microarray studies.
|
| Label |
biotin
|
| Label protocol |
Ribosomal RNA was first removed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA). This treated RNA was then converted to cDNA and subsequently processed and biotin-labeled.
|
| |
|
| Hybridization protocol |
cDNA was end-labeled with a biotinylated dideoxynucleotide using terminal transferase. Five and a half micrograms of biotinylated cDNA was added to a hybridization cocktail, loaded on a Human Exon 1.0 ST GeneChip and hybridized for 16 hours at 45 ºC and 60 rpm. Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.
|
| Scan protocol |
Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.
|
| Description |
RNA was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained with RMA and the Affymetrix CDF using Expression Console Version 1.0 software.
|
| Data processing |
Expression Console Version 1.1 (Affymetrix Inc.) was used to generate transcript-level gene expression estimates via the robust multichip average (RMA) algorithm using the Affymetrix CDF (Gene Level - Core: RMA Sketch). Gene symbols of transcript ids were retrieved using DAVID (http://david.abcc.ncifcrf.gov/). No filtering of genes was performed before statistical testing.
Quantile sketch normalized transcript level expression using the RMA algorithm with the Affymetrix CDF
|
| |
|
| Submission date |
Mar 01, 2011 |
| Last update date |
Sep 11, 2012 |
| Contact name |
Joshua David Campbell |
| E-mail(s) |
camp@bu.edu
|
| Organization name |
Boston University
|
| Street address |
72 East Concord St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE27597 |
A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK. |
|
