|
Status |
Public on Jun 03, 2010 |
Title |
Ptc+/- GNPs at P8, biological replicate 1 |
Sample type |
RNA |
|
|
Source name |
Ptc+/- GNPs
|
Organism |
Mus musculus |
Characteristics |
age: P8 disease state: normal tissue: n/a cell type: granule neuron precursor cells genotype: 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 |
Ptc+/- GNPs at P8, biological replicate 1
|
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 |
|