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Sample GSM566910 Query DataSets for GSM566910
Status Public on Mar 23, 2011
Title DNA of mouse 291 brain tumor corpus callosum, Female, 193 days
Sample type genomic
 
Channel 1
Source name tumor corpus callosum
Organism Mus musculus
Characteristics tissue: corpus callosum tumor
genotype: Pten, p53 knockout
gender: Female
Extracted molecule genomic DNA
Extraction protocol Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.
Label Cy5
Label protocol Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.
 
Channel 2
Source name normal genomic DNA with opposite sex to ch1
Organism Mus musculus
Characteristics sample type: normal genomic DNA with opposite sex to ch1
Extracted molecule genomic DNA
Extraction protocol Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.
Label Cy3
Label protocol Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.
 
 
Hybridization protocol Prior to hybridization, the test and reference probes were combined with 100 ug mouse fluorimetric Cot-1 (Invitrogen) and ethanol precipitated. Following centrifugation, the probes were resuspended in 110ul SlideHyb Buffer #3 (Ambion) containing 5ul of 100µg/ul Yeast tRNA (Invitrogen), heated to 95ºC for 5 minutes and incubated for 30 minutes at 37ºC to block repetitive elements on the probe. Hybridization was performed for 16 hours at 55ºC using a GeneMachine hybridization station (Genomic Solutions, Inc.) as described (Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125). After hybridization, the slides were automatically washed in the GeneMachines station with reducing concentrations of SSC and SDS. The final wash was 30 seconds in 0.1X SSC, followed by a two second 100 % ethanol dip. The slides were spun dry and scanned immediately at 5µm resolution using a GenePix 4000B laser scanner (Axon Inc.)
Scan protocol Slides were scanned on a GenePix 4000B laser Scanner (Axon Inc.) using GenePix Pro V6.0/1. Both lasers were set to 100% and the PMT was set to 500 for cy3 and 450 for cy5
Description tissue from mouse brain with high grade glioma.
Data processing Images were analyzed using Imagene 6.0 (BioDiscovery Inc.). The output of Image analysis was further processed by in-house developed programs. The log2 ratios of the test/control (values are not background subtracted) were normalized using a subgrid loess, with all flagged spots and clones on the sex chromosome are given a weight of zero. The mean of the replicate measures was taken and the final normalized log2 ratio was plotted against its genomic location.
 
Submission date Jul 15, 2010
Last update date Mar 23, 2011
Contact name Chunxu Qu
E-mail(s) chunxu.qu@stjude.org
Phone 9015952433
Organization name St Jude Children's Research Institute
Department Pathology
Lab Mullighan
Street address 262 Danny Thomas Pl
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL4714
Series (1)
GSE22927 Hierarchical synergy of Pten, p53 and Rb pathways in high-grade astrocytoma induced in adult brain

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (channel1/channel2)

Data table
ID_REF VALUE
RP23-271O17 -0.0045
RP23-320L20 0.0167
RP23-445L18 -0.0877
RP23-131C23 0.0971
RP23-32F6 -0.0094
RP23-297K4 -0.0021
RP23-422K10 -0.0929
RP23-69J22 -0.0681
RP23-294B12 -0.0336
RP23-410H10 0.1660
RP23-315F19 0.0697
RP23-144B15 -0.0383
RP23-480F21 0.0886
RP23-280K9 -0.1673
RP23-291G6 -0.0396
RP23-272K15 -0.0769
RP23-303L3 -0.0836
RP23-32B12 -0.0256
RP23-449G22 -0.0084
RP23-317K6 -0.0924

Total number of rows: 6062

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM566910_291_T.gpr.gz 1.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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