|
| Status |
Public on Feb 29, 2012 |
| Title |
dka212 |
| Sample type |
RNA |
| |
|
| Source name |
GFP negative spontaneous tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: GFP negative spontaneous tumor
|
| Treatment protocol |
Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.
|
| Growth protocol |
Myc-type tumors [dka201-203] were generated by orthotopic injection of Myc-infected cerebellar cells from Cdkn2c-/-, Trp53-/-, Atoh1-GFP mice into the cerebral cortex of immunocompromised nude mice. For Shh-type medulloblastomas [dka204-206], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] (Uziel et al.,2005 Genes Dev) were used. FACS-sorted GFP-positive [dka220-222] and GFP-negative [dka211, 212 and 219] populations were obtained from postnatal day 6 Cdkn2c-/-, Trp53-/-, Atoh1-GFP cerebella. Myc-type secondary tumors [dka223-225] were generated by orthotopic transplantation of cultured sphere cells from Myc-type primary tumors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared and labeled according to the standard Affymetrix one-Cycle protocol).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Data processing |
The data were analyzed with Partek Genomics Suite version 6.5 using the RMA method.
|
| |
|
| Submission date |
Oct 25, 2011 |
| Last update date |
Feb 29, 2012 |
| Contact name |
David Finkelstein |
| E-mail(s) |
david.finkelstein@stjude.org
|
| Phone |
9014953931
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
332 N. Lauderdale St.
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL11180 |
| Series (2) |
| GSE33200 |
A mouse model of the most aggressive subgroup of human medulloblastoma [HT_MG-430_PM] |
| GSE33201 |
A mouse model of the most aggressive subgroup of human medulloblastoma |
|
