GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM646944 Query DataSets for GSM646944
Status Public on Dec 01, 2011
Title IC Xenograft 645, biological rep 1
Sample type RNA
Source name GBM Subcutaneous Xenograft, Grown Intracranially
Organism Homo sapiens
Characteristics batch: 4
date of array: 2
line number: 20
line type: Subcutaneous Xenograft, Grown Intracranially
xenograft line: 645
Growth protocol Xenograft lines grown SC or IC until 200 mm^3, cell lines cultured to 70% confluence in either serum free or serum containing media
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Qiagen midi (xenograft), or mini (cell lines) kits. Xenograft tissue pulverized in liquid nitrogen and homogenized using a rotor-stator homogenizer
Label biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug of Total RNA (ExpressionAnalysis Techinical Manual, 2005, Affymetrix).
Hybridization protocol Following fragmentation, 10ug of biotinylated cRNA was hybridized for 16hr at 45C onto the Affymetrix Human Genome U133A Plus 2.0 Array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 according to standard protocols.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Data processing data normalized using Bioconductor in R using either RMA or MAS5.0 normalization protocols (RMA provided, see website for MAS5). Batch corrected expression values calculated by factor regression across Affymetrix doping and housekeeping controls
Submission date Dec 29, 2010
Last update date Dec 01, 2011
Contact name Jason W Reeves
Organization name Duke University
Lab Nevins, Joseph
Street address 101 Science Dr
City Durham
State/province North Carolina
ZIP/Postal code 27710
Country USA
Platform ID GPL571
Series (1)
GSE26344 In vitro models of glioblastoma (GBM)

Data table header descriptions
VALUE RMA signal intensity

Data table
1007_s_at 9.6911
1053_at 8.1964
117_at 5.0459
121_at 6.8354
1255_g_at 3.3865
1294_at 5.3407
1316_at 4.5129
1320_at 5.1384
1405_i_at 3.4572
1431_at 3.2607
1438_at 6.8367
1487_at 7.2618
1494_f_at 4.9716
1598_g_at 7.7744
160020_at 7.1747
1729_at 6.7197
1773_at 6.8087
177_at 4.6356
179_at 8.1848
1861_at 6.1789

Total number of rows: 22277

Table truncated, full table size 391 Kbytes.

Supplementary file Size Download File type/resource
GSM646944.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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