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Sample GSM1009086 Query DataSets for GSM1009086
Status Public on Sep 27, 2012
Title Tumor 2_37C @ 5 mins
Sample type RNA
 
Source name Tumor 2_37C @ 5 mins
Organism Homo sapiens
Characteristics tissue: VHL Clear Cell Renal Cell Carcinoma
patient: Tumor 2
treatment: 37C @ 5 mins
Treatment protocol 10 renal tumors were divided and treated under the above listed conditions and snap frozen at 5, 30, 60, 120 and 240 minutes after surgical resection
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using GeneChip Two-Cycle cDNA Target Synthesis Kit (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 olgionucleotide array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol Each array was washed, stained and scanned by the Affymetrix GeneChip 3000 Scanner. Raw intensities for each probe were stored as .DAT and .CEL files by the GeneChip Operating Software v1.4 (Affymetrix Inc, Santa Clara, CA USA).
Description Gene expression data from tumor 2 at ischemic conditions
Data processing Complete analyses of array data were carried out in BRB-Array Tools v3.7 (http://linus.nci.nih.gov/BRB-ArrayTools.html)
Processed/Filtered and Log2_transformed array intensities
 
Submission date Sep 25, 2012
Last update date Sep 27, 2012
Contact name Nick Liu
E-mail(s) nick.liu@gmail.com
Organization name Indiana University Hospital
Department Department of Urology
Street address 535 Barnhill Drive Suite 420
City INDIANAPOLIS
State/province Indiana
ZIP/Postal code 46202
Country USA
 
Platform ID GPL570
Series (1)
GSE41137 Impact of Ischemia and Procurement Conditions on Gene Expression in Renal Cell Carcinoma

Data table header descriptions
ID_REF
VALUE log2 GCRMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 9.573698997
1053_at 7.762048244
117_at 6.479043961
121_at 9.004253387
1255_g_at 2.901943922
1294_at 8.080436707
1316_at 5.497814655
1320_at 3.693255186
1405_i_at 11.35276413
1431_at 3.352101088
1438_at 5.423314571
1487_at 8.082800865
1494_f_at 5.407536507
1552256_a_at 9.178420067
1552257_a_at 7.148974895
1552258_at 4.889382839
1552261_at 3.575381994
1552263_at 7.350520611
1552264_a_at 7.047950745
1552266_at 3.408593655

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1009086_NL_RCC_11_20_08_3-1-N.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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