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Sample GSM441428 Query DataSets for GSM441428
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

Data table header descriptions
VALUE Gene level expression values from dChip

Data table
6747308 423
6747309 1087
6747314 915
6747326 2
6747343 338
6747354 612
6747364 489
6747471 527
6747472 54
6747478 148
6747497 69
6747515 215
6747577 43
6747641 76
6747696 6
6747786 284
6747805 225
6747837 357
6747839 18
6747861 16

Total number of rows: 16317

Table truncated, full table size 185 Kbytes.

Supplementary file Size Download File type/resource
GSM441428_MB2_MoEx1_0-st-v1.CEL.gz 22.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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