NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM821975 Query DataSets for GSM821975
Status Public on Feb 29, 2012
Title dka205
Sample type RNA
 
Source name Shh tumors
Organism Mus musculus
Characteristics tissue type: Shh 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 9.04624
1415671_PM_at 10.9013
1415672_PM_at 10.1878
1415673_PM_at 8.43535
1415674_PM_a_at 9.21409
1415675_PM_at 8.75586
1415676_PM_a_at 10.8389
1415677_PM_at 7.27525
1415678_PM_at 9.82301
1415679_PM_at 10.6995
1415680_PM_at 8.77657
1415681_PM_at 9.56353
1415682_PM_at 8.36414
1415683_PM_at 10.161
1415684_PM_at 7.18735
1415685_PM_at 8.78061
1415686_PM_at 8.86699
1415687_PM_a_at 9.97492
1415688_PM_at 10.1393
1415689_PM_s_at 9.56241

Total number of rows: 45141

Table truncated, full table size 982 Kbytes.




Supplementary file Size Download File type/resource
GSM821975_dka205-htmg430pm.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap