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Sample GSM335300 Query DataSets for GSM335300
Status Public on Dec 27, 2008
Title Renal Clear Cell Carcinoma_TB3852
Sample type genomic
 
Source name DNA from Renal Clear Cell Carcinoma
Organism Homo sapiens
Characteristics Group: H1H2
VHL_Analysis: Exon: 1
VHL_Analysis: Mutation_Type: Missense
VHL_Analysis: Methylation: Unmethylated
VHL_Analysis: mRNA_Change: c.193T>C
VHL_Analysis: Protein_Change: p.Ser65Pro
VHL_Analysis: Copy_Number: 1
c-Myc_Copy_Number: 2
Gender: F
Age: 76
Fuhrman: 3
T_score: 1a
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 3.357 0.05 -0.4224
MitoA10551G-13273286_T_F_IFB1141639111:0 3.357 0.232 -0.6418
MitoA11252G-13273288_B_R_IFB1141661584:0 3.357 0.237 -0.6832
MitoA11468G-13273289_B_R_IFB1141719645:0 3.357 0.227 -0.7712
MitoA11813G-13273292_T_F_IFB1141667833:0 3.357 0.386 -0.4742
MitoA12309G-13273294_T_F_IFB1141664161:0 3.357 0.168 -0.4898
MitoA13106G-13273298_B_R_IFB1141641623:0 1.548 0.064 0.0401
MitoA13264G-13273299_T_F_IFB1141660858:0 3.357 0.36 -0.8571
MitoA13781G-13273301_T_F_IFB1141687043:0 1.304 0.101 0.1409
MitoA14234G-13273304_T_F_IFB1141674277:0 2.66 0.083 -0.2712
MitoA14583G-13273306_T_F_IFB1141688843:0 2.048 0.024 -0.1295
MitoA15219G-13273311_T_F_IFB1141717824:0 3.19 0.53 -0.4726
MitoA15245G-13273312_B_R_IFB1141677374:0 2.304 0.246 -0.0823
MitoA15302G-13273313_T_F_IFB1141686491:0 0.542 2.382 -0.1592
MitoA15759G-13273316_B_R_IFB1141715135:0 3.357 0.222 -0.8268
MitoA15925G-13273318_T_F_IFB1141694300:0 3.357 0.302 -0.1067
MitoA16163G-13273319_T_F_IFB1141711520:0 3.357 0.625 -0.6867
MitoA16164G-13273320_T_F_IFB1141715312:0 3.357 0.155 -0.3556
MitoA1738G-13273322_T_F_IFB1141639534:0 3.357 0.269 -0.7558
MitoA3349G-13273328_T_F_IFB1141711832:0 3.357 0.411 -0.9026

Total number of rows: 561466

Table truncated, full table size 28952 Kbytes.




Supplementary file Size Download File type/resource
GSM335300.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table
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