|
| Status |
Public on Feb 29, 2012 |
| Title |
dka047 |
| Sample type |
RNA |
| |
|
| Source name |
Mycn tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: p53-/-, Cdkn2c-/-, Math1-GFP infected with mMycn/mRFP
|
| Treatment protocol |
Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.
|
| Growth protocol |
For Shh-type medulloblastoma [dka001-005, 009, 033 and 034] and [dka050-057], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] and [Cdkn2c-/-; Ptch1+/-] (Uziel et al.,2005 Genes Dev) were used, respectively. For Myc [dka010-022, 037, 046, 049 and 058-71] and Mycn [dka023-032, 036 and 047] were generated by orthotopic injection of either Myc or Mycn overexpression in Cdkn2c-/-, Trp53-/- cerebellar cells into immunocompromised nude mice. For Wnt-type medulloblastomas [pgr003, 016 and 066], spontaneously developed tumors from CTNNB1+/lox (ex3); BLBP-Cre; Trp53Fl/Fl (Gibson et al., Nature, 2010) were removed for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.
|
| Label |
Biotin (One cycle kit)
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol). Some samples were amplified and labelled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction.
|
| |
|
| 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 batch correction for amplficiation assay followed using the three repeated samples assayed by both methods in STATA/SE 11. Data provided in the spreadsheet is the corrected data.
|
| |
|
| 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 |
GPL1261 |
| Series (2) |
| GSE33199 |
A mouse model of the most aggressive subgroup of human medulloblastoma [Mouse430_2] |
| GSE33201 |
A mouse model of the most aggressive subgroup of human medulloblastoma |
|
