NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM646941 Query DataSets for GSM646941
Status Public on Dec 01, 2011
Title Cell Line D54TR, biological rep 1
Sample type RNA
 
Source name GBM Serum Cell Line
Organism Homo sapiens
Characteristics batch: 4
date of array: 2
line number: 14
line type: Serum Cell Line
cell line: D54TR
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
E-mail(s) jwr11@duke.edu
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
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1007_s_at 9.7760
1053_at 7.0350
117_at 4.9421
121_at 7.4054
1255_g_at 3.4682
1294_at 5.8129
1316_at 4.4851
1320_at 5.6913
1405_i_at 3.4683
1431_at 3.3701
1438_at 6.0747
1487_at 7.5543
1494_f_at 4.8074
1598_g_at 7.4980
160020_at 6.7921
1729_at 7.3192
1773_at 6.0488
177_at 5.4527
179_at 8.0252
1861_at 6.6996

Total number of rows: 22277

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM646941.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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