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Sample GSM646960 Query DataSets for GSM646960
Status Public on Dec 01, 2011
Title Xenograft 475, biological rep 1
Sample type RNA
 
Source name GBM Subcutaneous Xenograft
Organism Homo sapiens
Characteristics batch: 5
date of array: 2
line number: 35
line type: Subcutaneous Xenograft
xenograft line: 475
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 9.4297
1053_at 8.2738
117_at 4.7289
121_at 7.1705
1255_g_at 3.4019
1294_at 6.3763
1316_at 4.7606
1320_at 5.5232
1405_i_at 3.5995
1431_at 3.3268
1438_at 6.4259
1487_at 6.9220
1494_f_at 4.7785
1598_g_at 7.0995
160020_at 8.1981
1729_at 7.0152
1773_at 6.3764
177_at 4.7863
179_at 8.1876
1861_at 6.1079

Total number of rows: 22277

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM646960.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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