|
| Status |
Public on Jul 27, 2009 |
| Title |
S.7.3 |
| Sample type |
RNA |
| |
|
| Source name |
S.7. SM/J ear tissue from around the injury site, 7 days post-injury
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ear tissue
strain: SM/J
stress: ear punch
time: 7 days post-injury
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol according to manufacturer's protocol (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Pipette 2 mL Block E1 buffer + streptavidin-Cy3 into fresh Wash Tray(s).
Transfer the BeadChip, face up into Wash Tray(s) on rocker.
Place cover on tray and rock at medium speed for 10 minutes.
|
| |
|
| Hybridization protocol |
Illumina Hyb protocol
|
| Scan protocol |
Illumina scan protocol
|
| Description |
ear tissue from mouse from around the injury site, 7 days post-injury
|
| Data processing |
1. The raw data of the spot density was extracted from Illumina BeadStudio software.
2. Check samples outlier.
3. Filter out genes that had poor detection in all samples ( detection p-value>0.05 in all samples) or genes that have at least <1.2 fold change between at least 2 samples
4. Quantile normalization for the filtering data.
5. Apply one-way ANOVA on the quantile normalization data to find out the significant gene data.
|
| |
|
| Submission date |
Jul 17, 2009 |
| Last update date |
Jul 26, 2009 |
| Contact name |
Louise C Showe |
| E-mail(s) |
lshowe@wistar.org
|
| Phone |
215-898-3791
|
| Organization name |
The Wistar Institute
|
| Lab |
Dr. Louise Showe
|
| Street address |
3601 Spruce St
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE17168 |
Genetic loci that regulate healing and regeneration in LG/J and SM/J mice |
|
