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Sample GSM215422 Query DataSets for GSM215422
Status Public on Aug 07, 2007
Title GBM_1507_34705-34696
Sample type RNA
 
Source name tumor tissue GBM, patient tag 1507, experiment 34705-34696
Organism Homo sapiens
Characteristics Tumor tissue: high grade glioblastoma
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tumor samples using a TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA) and was followed by a cleanup on a RNeasy column (Qiagen, Hilden, Germany).
Label biotin
Label protocol cRNA probes were generated using standard Affymetrix protocols.
 
Hybridization protocol Aliquots of each sample were hybridized to U133A oligonucleotide microarray using standard Affymetrix protocols.
Scan protocol The chips were scanned using the GeneArray scanner (Affymetrix) using standard Affymetrix protocols.
Description All RNA samples had a 28S/18S ratio over 1.5 with no evidence of degradation. All scanned images were visually inspected for surface defects. Quality Control assessment of array data was performed using GCOS v1.4 (Affymetrix, Santa Clara, Ca) and Array Assist v5.0 build 30237 (Stratagene, La Jolla, Ca). Hybridization and Poly-A controls were within expected parameters, and 3'/5' ratios for actin and GAPDH were below 3 (mean Beta Actin 3'/5' = 1.53 and mean GAPDH 3'/5' = 1.02). GCOS v1.4 Expression Reports also revealed expected Call percentages (Present: 48% to 62%; Absent: 36% to 49%; Marginal: 1.5% to 1.9%). All arrays were within 1.5 fold of each other in overall intensity.
Data processing The CEL files generated by the Affymetrix Microarray Suite (MAS 5.0) were converted into DCP files using the DNA-Chip Analyzer (dCHIP 1.3).
 
Submission date Aug 03, 2007
Last update date Aug 14, 2011
Contact name Tsunglin Liu
E-mail(s) tliu@lifesci.ucsb.edu
Organization name Neuroscience Research Institute
Street address R5157, BIO II, UCSB
City Santa Barbara
State/province CA
ZIP/Postal code 93106
Country USA
 
Platform ID GPL96
Series (1)
GSE8692 Endogeneous mRNA level fluctuations in various brain tumor cells

Data table header descriptions
ID_REF
VALUE dCHIP normalized signal intensity
ABS_CALL dCHIP absence call

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 73.755 P
AFFX-BioB-M_at 69.894 P
AFFX-BioB-3_at 62.346 P
AFFX-BioC-5_at 204.709 P
AFFX-BioC-3_at 156.207 P
AFFX-BioDn-5_at 314.475 P
AFFX-BioDn-3_at 986.101 P
AFFX-CreX-5_at 2316.736 P
AFFX-CreX-3_at 2605.798 P
AFFX-DapX-5_at 52.07 A
AFFX-DapX-M_at 31.472 A
AFFX-DapX-3_at 12.915 A
AFFX-LysX-5_at 27.641 A
AFFX-LysX-M_at 67.492 A
AFFX-LysX-3_at 32.179 A
AFFX-PheX-5_at 1 A
AFFX-PheX-M_at 6.647 A
AFFX-PheX-3_at 51.868 A
AFFX-ThrX-5_at 15.075 A
AFFX-ThrX-M_at 14.973 A

Total number of rows: 22283

Table truncated, full table size 441 Kbytes.




Supplementary file Size Download File type/resource
GSM215422.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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