|
| Status |
Public on May 22, 2014 |
| Title |
WTC 76 PBS treated |
| Sample type |
RNA |
| |
|
| Source name |
WT_lung_PBS_control
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57/129S
genotype/variation: Fra-1+/+; wild type
gender: female
age: 2 months
treated with: 30 µl of PBS for 5 days
tissue: lung
|
| Treatment protocol |
30 µl of PBS or PBS containing bleomycin (0.075U/mouse) instilled intratracheally for 5 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using Qiagen Rneasy micro kit according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
First strand cDNA synthesis, 2nd strand cDNA, IVT, 2nd cycle cDNA synthesis, hydrolysis of cRNA, clean up of the 2nd cycle cDNA, fragmentation of cDNA, and labeling of fragmented single strand cDNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 80 µl of hybridization cocktail containing 2.75 ug of fragmented cRNA placed on chip - Hybridized for overnight. The whole hybridization was performed according to Gene Chip Hybridization, Wash and Stain Kit.
|
| Scan protocol |
Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
|
| Description |
WTC76
|
| Data processing |
Data extraction was processed by Affymetrix MoGene 1.0ST v1 Array. The raw probe signal intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish, using the Affymetrix Power Tools. We considered a transcript cluster (gene-level) to be reliably expressed in a sample if the Affymetrix implemented DABG (detection above ground) p-value was less than 0.05. We used local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression in a comparison.
|
| |
|
| Submission date |
Jan 23, 2013 |
| Last update date |
May 22, 2014 |
| Contact name |
Rajasekaran Subbiah |
| E-mail(s) |
[email protected]
|
| Phone |
(312)4133237
|
| Fax |
(312)9967583
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Pediatrics
|
| Lab |
Dr. Reddy's lab
|
| Street address |
909, South Wolcott Ave, Room # 7160
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE43695 |
Comparative analysis of gene expression in Fra-1+/+ and Fra-1-/- mice lung |
|
