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Sample GSM335293 Query DataSets for GSM335293
Status Public on Dec 27, 2008
Title Renal Clear Cell Carcinoma_TB4105
Sample type genomic
 
Source name DNA from Renal Clear Cell Carcinoma
Organism Homo sapiens
Characteristics Group: H1H2
VHL_Analysis: Exon: 2
VHL_Analysis: Mutation_Type: Frameshift
VHL_Analysis: Methylation: Unmethylated
VHL_Analysis: mRNA_Change: c.392_397del8
VHL_Analysis: Protein_Change: p.Gln132FS
VHL_Analysis: Copy_Number: 1
c-Myc_Copy_Number: 2
Gender: M
Age: 65
Fuhrman: 3
T_score: 3a
M: 0
Extracted molecule genomic DNA
Extraction protocol Frozen RCCs were obtained through the Collaborative Human Tissue Network
H&E staining was performed on each sample, and they were confirmed to have clear cell morphology, and be more than 70% tumor
The Wizard® Genomic DNA Purification Kit from Promega was used to extract genomic DNA from the tumors
Label Illumina standard protocol
Label protocol Labelling was done according to Illumina's standard protocol
 
Hybridization protocol Hybridization was done according to Illumina's standard protocol
Scan protocol The chips were scanned using Illuminaa's standard scanner.
Description Array CGH data from Human RCC sample
Data processing The data were extracted using Illumina's Bead Studio software and analyzed in Partek as described in the paper Gordan et al. Cancer Cell (2008).
 
Submission date Oct 20, 2008
Last update date Oct 22, 2008
Contact name Bradley Wubbenhorst
E-mail(s) bwubb@mail.med.upenn.edu
Phone 215-898-0248
Organization name University of Pennsylvannia
Street address 421 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL6982
Series (1)
GSE13282 Array CGH analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

Data table header descriptions
ID_REF
X normalized X intensity
Y normalized Y intensity
VALUE log R Ratio (Illumina standard header)

Data table
ID_REF X Y VALUE
MitoA10045G-13273284_B_R_IFB1141652022:0 3.408 0.051 -0.4007
MitoA10551G-13273286_T_F_IFB1141639111:0 3.95 0.28 -0.4046
MitoA11252G-13273288_B_R_IFB1141661584:0 4.044 0.201 -0.4432
MitoA11468G-13273289_B_R_IFB1141719645:0 4.023 0.192 -0.5567
MitoA11813G-13273292_T_F_IFB1141667833:0 3.485 0.387 -0.4252
MitoA12309G-13273294_T_F_IFB1141664161:0 3.395 0.204 -0.4601
MitoA13106G-13273298_B_R_IFB1141641623:0 1.209 0.046 -0.3205
MitoA13264G-13273299_T_F_IFB1141660858:0 4.069 0.334 -0.6127
MitoA13781G-13273301_T_F_IFB1141687043:0 0.68 0.065 -0.7739
MitoA14234G-13273304_T_F_IFB1141674277:0 2.249 0.067 -0.515
MitoA14583G-13273306_T_F_IFB1141688843:0 2.098 0.028 -0.093
MitoA15219G-13273311_T_F_IFB1141717824:0 3.42 0.533 -0.3849
MitoA15245G-13273312_B_R_IFB1141677374:0 2.061 0.215 -0.2462
MitoA15302G-13273313_T_F_IFB1141686491:0 0.495 2.443 -0.0853
MitoA15759G-13273316_B_R_IFB1141715135:0 4.014 0.19 -0.5945
MitoA15925G-13273318_T_F_IFB1141694300:0 3.449 0.242 -0.0942
MitoA16163G-13273319_T_F_IFB1141711520:0 3.994 0.556 -0.4945
MitoA16164G-13273320_T_F_IFB1141715312:0 3.018 0.176 -0.4925
MitoA1738G-13273322_T_F_IFB1141639534:0 4.069 0.244 -0.5058
MitoA3349G-13273328_T_F_IFB1141711832:0 3.743 0.356 -0.781

Total number of rows: 561466

Table truncated, full table size 28989 Kbytes.




Supplementary file Size Download File type/resource
GSM335293.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table
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