|
| Status |
Public on Jun 14, 2011 |
| Title |
v1 |
| Sample type |
RNA |
| |
|
| Source name |
ventilation 1
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD/shi
age: 6-12 weeks
tissue: whole lung
ventilation: yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lung tissues with Trizol (Invitrogen). RNA clean-up and DNase I treatment was performed with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 1
|
| Data processing |
Microarray expression profiles were generated using Illumina REF8 mouse arrays according to the manufacturer’s protocol. The data were normalised using quantile normalisation with IlluminaGUI in R. For statistical analysis we applied Welch's two-sample t-tests to find genes with significant expression changes. The P values from the t-tests were adjusted for multiple testing using the false discovery rate (FDR) controlling procedure of Benjamini. Genes which have the adjusted P values less than 0.05 were considered significantly changed .
|
| |
|
| Submission date |
Jun 13, 2011 |
| Last update date |
Jun 14, 2011 |
| Contact name |
Tamas Dolinay |
| E-mail(s) |
tdolinay@hotmail.com
|
| Phone |
4125278764
|
| Organization name |
University of Pennsylvania
|
| Department |
Bioengineering
|
| Lab |
Susan Margulies
|
| Street address |
220 S. 33rd St., Towne building, Room 390
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE29920 |
Mouse gene expression profiling in ventilator-induced lung injury |
|
