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Sample GSM821977 Query DataSets for GSM821977
Status Public on Feb 29, 2012
Title dka211
Sample type RNA
 
Source name GFP negative spontaneous tumor
Organism Mus musculus
Characteristics tissue type: GFP negative spontaneous tumor
Treatment protocol Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.
Growth protocol Myc-type tumors [dka201-203] were generated by orthotopic injection of Myc-infected cerebellar cells from Cdkn2c-/-, Trp53-/-, Atoh1-GFP mice into the cerebral cortex of immunocompromised nude mice. For Shh-type medulloblastomas [dka204-206], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] (Uziel et al.,2005 Genes Dev) were used. FACS-sorted GFP-positive [dka220-222] and GFP-negative [dka211, 212 and 219] populations were obtained from postnatal day 6 Cdkn2c-/-, Trp53-/-, Atoh1-GFP cerebella. Myc-type secondary tumors [dka223-225] were generated by orthotopic transplantation of cultured sphere cells from Myc-type primary tumors.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.
Label Biotin
Label protocol Biotinylated cRNA were prepared and labeled according to the standard Affymetrix one-Cycle protocol).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Data processing The data were analyzed with Partek Genomics Suite version 6.5 using the RMA method.
 
Submission date Oct 25, 2011
Last update date Feb 29, 2012
Contact name David Finkelstein
E-mail(s) david.finkelstein@stjude.org
Phone 9014953931
Organization name St Jude Children's Research Hospital
Department Computational Biology
Street address 332 N. Lauderdale St.
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL11180
Series (2)
GSE33200 A mouse model of the most aggressive subgroup of human medulloblastoma [HT_MG-430_PM]
GSE33201 A mouse model of the most aggressive subgroup of human medulloblastoma

Data table header descriptions
ID_REF
VALUE RMA log2 signal intensity

Data table
ID_REF VALUE
1415670_PM_at 8.69743
1415671_PM_at 10.6513
1415672_PM_at 10.7494
1415673_PM_at 8.41607
1415674_PM_a_at 9.08547
1415675_PM_at 8.7239
1415676_PM_a_at 10.6452
1415677_PM_at 8.84081
1415678_PM_at 9.5418
1415679_PM_at 10.8459
1415680_PM_at 8.41141
1415681_PM_at 9.51462
1415682_PM_at 7.79052
1415683_PM_at 10.0407
1415684_PM_at 7.63661
1415685_PM_at 8.65575
1415686_PM_at 9.36976
1415687_PM_a_at 11.4613
1415688_PM_at 10.11
1415689_PM_s_at 9.51836

Total number of rows: 45141

Table truncated, full table size 982 Kbytes.




Supplementary file Size Download File type/resource
GSM821977_dka211-htmg430pm.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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