|
| Status |
Public on Jun 03, 2010 |
| Title |
Medulloblastoma, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Gli1FLAG;Ptc+/- tumor
|
| Organism |
Mus musculus |
| Characteristics |
age: Adult
disease state: medulloblastoma
tissue: medulloblastoma
cell type: n/a
genotype: Gli1FLAG;Ptc+/-
|
| Treatment protocol |
not applicable
|
| Growth protocol |
RosaGli1-FLAG c/c mice (Vokes et al., 2007) were crossed with Math1Cre (Matei et al., 2005) mice and litters were taken at P8 to isolate Gli1-FLAG-expressing GNPs. Ptc+/- GNPs were purified from P8 Ptc+/- mice (Goodrich et al., 1997). Cerebellums were dissected into PBS and GNPs were isolated as previously described (Wechsler-Reya and Scott 1999). Medulloblastoma tumors were isolated from RosaGli1-FLAG c/c;Math1-Cre;Ptc+/- mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol reagent (Invitrogen). Ribosomal RNA reduction was performed using RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). cDNA synthesis and amplification were done using GeneChip WT cDNA Synthesis Kit (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
Samples were fragmented and biotin-labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized for 16 hours at 45° at 60rpm, according to manufacturer's instructions (Affymetrix).
|
| Scan protocol |
Affymetrix GeneChiP Scanner 3000 7G
|
| Description |
medulloblastoma, biological replicate 2
|
| Data processing |
Data were processed using GeneBASE software. MAT background correction was applied to probe intensities. Gene expression indices were calculated from the background-corrected core probe intensities using the dChip model. Differential gene expression was determined using SAM analysis.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps
|
| |
|
| Submission date |
Aug 18, 2009 |
| Last update date |
Jun 03, 2010 |
| Contact name |
Eunice Lee |
| Organization name |
Stanford University
|
| Department |
Developmental Biology
|
| Lab |
Matthew Scott
|
| Street address |
318 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL6096 |
| Series (2) |
| GSE17702 |
Gene expression profiles of murine granule neuron precursors and medulloblastoma |
| GSE17719 |
Gli1 regulatory networks in granule neuron precursor and medulloblastoma cells |
|
