|
| Status |
Public on Dec 11, 2015 |
| Title |
Mouse Brain AT/RT, sample 2 |
| Sample type |
RNA |
| |
|
| Source name |
Brain tumor
|
| Organism |
Mus musculus |
| Characteristics |
tumor type: AT/RT
|
| Treatment protocol |
Mice were sacrifced by cervical dislocation after intraperitoneal injection with ketamine and xylazine. Following dissection, brain tissues were isolated for RNA extraction
|
| Growth protocol |
Snf5F/F/p53L/L/GFAP-Cre mice transgenic mice for AT/RT samples, and Ptc1+/- p53+/- (n = 2) and Ptc1+/- p53-/- (n = 3) transgenic mice for medulloblastoma samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the MessageAmp Premier Amplification Kit protocol using 200 ng of total RNA as input (MessageAmp Premier Ampification Kit Manual, Revision G, Ambion).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
|
| Description |
Mouse model of AT/RT brain tumor
|
| Data processing |
The CEL files were processed using the RMA method (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/12582260) and a custom library provided by the BRAINARRAY project, version 18.0.0 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/entrezg.asp).
|
| |
|
| Submission date |
May 06, 2015 |
| Last update date |
Dec 11, 2015 |
| Contact name |
Jessica Mei Y. Ng |
| E-mail(s) |
ngj@email.chop.edu
|
| Organization name |
The Children's Hopsital of Philadelphia
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
Colket Translational Research Bldg (Rm 4059) 3501 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19559 |
| Series (1) |
| GSE68627 |
Snf5F/Fp53L/LGFAP-Cre tumors and human AT/RT show similar gene expression signatures |
|
