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Sample GSM2080624 Query DataSets for GSM2080624
Status Public on Jun 01, 2018
Title Z1_Astrocytoma_7
Sample type RNA
 
Source name malignant glioma
Organism Mus musculus
Characteristics genotype: hGFAP-cre;p53KO/+;Nf1+/flox
phenotype: malignant glioma
Treatment protocol Mice carry various genotypic configurations as indicated for each case.
Growth protocol Cell cultures were prepared based on a previously published protocol (Wang et al., Cell 150, 816-830, 2012), and chromosome metaphase assays were performed according to an established protocol.
Extracted molecule total RNA
Extraction protocol Total RNAs and genomic DNAs were extracted from wild-type control brain tissues, high-grade gliomas and MBs by using AllPrep DNA/RNA Mini Kit (Qiagen). cDNA synthesis was performed using QuantiTect Reverse Transcription Kit (Qiagen) and RT-PCR was performed using SYBR Select Master Mix (Applied Biosystems).
Label biotin
Label protocol Complementary RNA synthesis and labeling/hybridization/scanning of Mouse Genome 430 2.0 microarrays using GeneChip products (Affymetrix) was done as described in the GeneChip manual (see below fields).
 
Hybridization protocol Hybridization was performed following a published protocol (Miller D et al, Curr. Protoc. Hum. Genet. 2012. PMID: 18633976)
Scan protocol GeneChips were scanned according to manufacturer recommendation
Description phenotype: malignant glioma
Data processing The CEL files were preprocessed and normalized by the aroma package using a custom CDF file from AffyProbeMiner (GPL9523)
 
Submission date Mar 04, 2016
Last update date Jun 02, 2018
Contact name Yuan Zhu
E-mail(s) YZhu@childrensnational.org
Organization name Children's National Medical Center
Street address 111 Michigan Ave NW
City Washington DC
State/province DC
ZIP/Postal code 20010
Country USA
 
Platform ID GPL9523
Series (1)
GSE78895 Rictor/mTORC2 signaling has opposing functions in adult glioma and childhood SHH medulloblastoma

Data table header descriptions
ID_REF
VALUE log2 scale, normalized signal intensity

Data table
ID_REF VALUE
AFFYCUSTOMHF1 6.323665999
AFFYCUSTOMHF10 6.568525479
AFFYCUSTOMHF100 10.85575988
AFFYCUSTOMHF1000 5.613313877
AFFYCUSTOMHF10000 12.35574884
AFFYCUSTOMHF10001 6.079285385
AFFYCUSTOMHF10002 7.485551239
AFFYCUSTOMHF10003 7.695047709
AFFYCUSTOMHF10004 8.967345977
AFFYCUSTOMHF10007 9.524796951
AFFYCUSTOMHF10008 7.16218078
AFFYCUSTOMHF10009 6.757597745
AFFYCUSTOMHF1001 8.034914798
AFFYCUSTOMHF10010 9.181585262
AFFYCUSTOMHF10011 5.657257164
AFFYCUSTOMHF10013 8.078709495
AFFYCUSTOMHF10014 7.902164116
AFFYCUSTOMHF10015 7.681771149
AFFYCUSTOMHF10016 12.21634993
AFFYCUSTOMHF10017 6.75372183

Total number of rows: 18328

Table truncated, full table size 526 Kbytes.




Supplementary file Size Download File type/resource
GSM2080624_Z1_Astrocytoma_7.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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