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Sample GSM646952 Query DataSets for GSM646952
Status Public on Dec 01, 2011
Title Cell Line D54P, biological rep 1
Sample type RNA
Source name GBM Serum Cell Line
Organism Homo sapiens
Characteristics batch: 5
date of array: 2
line number: 13
line type: Serum Cell Line
cell line: D54P
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 9.2266
1053_at 7.7846
117_at 4.8853
121_at 7.3722
1255_g_at 3.4589
1294_at 5.7502
1316_at 4.6798
1320_at 5.0976
1405_i_at 3.6085
1431_at 3.2069
1438_at 6.0557
1487_at 7.5544
1494_f_at 4.7977
1598_g_at 7.9719
160020_at 6.5068
1729_at 6.9631
1773_at 5.8710
177_at 5.4691
179_at 8.1811
1861_at 7.3608

Total number of rows: 22277

Table truncated, full table size 391 Kbytes.

Supplementary file Size Download File type/resource
GSM646952.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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