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Sample GSM647020 Query DataSets for GSM647020
Status Public on Dec 01, 2011
Title Cell Line U138OTR, biological rep 1
Sample type RNA
 
Source name GBM Serum Cell Line
Organism Homo sapiens
Characteristics batch: 10
date of array: 3
line number: 46
line type: Serum Cell Line
cell line: U138OTR
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 8.8869
1053_at 8.2349
117_at 4.8662
121_at 7.5969
1255_g_at 3.4209
1294_at 6.1318
1316_at 4.8787
1320_at 5.4888
1405_i_at 3.4267
1431_at 3.1967
1438_at 6.1528
1487_at 6.9493
1494_f_at 5.0311
1598_g_at 7.9491
160020_at 8.0402
1729_at 7.3499
1773_at 5.8459
177_at 4.7875
179_at 8.3405
1861_at 6.6548

Total number of rows: 22277

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM647020.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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