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Status |
Public on Dec 11, 2015 |
Title |
Mouse Brain AT/RT, sample 4 |
Sample type |
RNA |
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Source name |
Brain tumor
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Organism |
Mus musculus |
Characteristics |
tumor type: AT/RT
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Treatment protocol |
Mice were sacrifced by cervical dislocation after intraperitoneal injection with ketamine and xylazine. Following dissection, brain tissues were isolated for RNA extraction
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Growth protocol |
Snf5F/F/p53L/L/GFAP-Cre mice transgenic mice for AT/RT samples, and Ptc1+/- p53+/- (n = 2) and Ptc1+/- p53-/- (n = 3) transgenic mice for medulloblastoma samples
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit.
|
Label |
Biotin
|
Label protocol |
Biotinylated cRNA were prepared according to the MessageAmp Premier Amplification Kit protocol using 200 ng of total RNA as input (MessageAmp Premier Ampification Kit Manual, Revision G, Ambion).
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Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
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Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
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Description |
Mouse model of AT/RT brain tumor
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Data processing |
The CEL files were processed using the RMA method (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/12582260) and a custom library provided by the BRAINARRAY project, version 18.0.0 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/entrezg.asp).
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Submission date |
May 06, 2015 |
Last update date |
Dec 11, 2015 |
Contact name |
Jessica Mei Y. Ng |
E-mail(s) |
ngj@email.chop.edu
|
Organization name |
The Children's Hopsital of Philadelphia
|
Department |
Pathology and Laboratory Medicine
|
Street address |
Colket Translational Research Bldg (Rm 4059) 3501 Civic Center Blvd
|
City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
|
|
Platform ID |
GPL19559 |
Series (1) |
GSE68627 |
Snf5F/Fp53L/LGFAP-Cre tumors and human AT/RT show similar gene expression signatures |
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