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Sample GSM1063437 Query DataSets for GSM1063437
Status Public on Oct 16, 2014
Title M2P
Sample type genomic
 
Channel 1
Source name primary ccRCC
Organism Homo sapiens
Characteristics tissue: primary ccRCC
age: 76
Sex: male
site: kidney
Stage: T1bN0M1
Extracted molecule genomic DNA
Extraction protocol standard proteinase K-digestion method
Label Cy5
Label protocol Agilent Genomic DNA Labeling Kit Plus(Agilent)
 
Channel 2
Source name normal renal cortex
Organism Homo sapiens
Characteristics tissue: normal renal cortex
Sex: male
Extracted molecule genomic DNA
Extraction protocol standard proteinase K-digestion method
Label Cy3
Label protocol Agilent Genomic DNA Labeling Kit Plus(Agilent)
 
 
Hybridization protocol dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65C for 24 h
Scan protocol A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm
Description normal renal cortex obtained from each patient was used as the source of control DNA
Data processing Microarray images were analyzed by using FEATURE EXTRACTION v.9.1.3.1, v.9.5.1.1 or v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_91 or CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). Following normalization of the raw data, the log2ratio of Cy5 (tumor) to Cy3 (Control) was calculated. Aberrant regions were determined by the Aberration Detection Method-2 algorithm at a threshold of 6.0 in DNA Analytics. To detect gains and losses of chromosomal regions, we set the values of parameters for aberration filters as follows: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.10, maximum number of aberrant regions 10000, and percentage penetrance per feature 0.
 
Submission date Jan 14, 2013
Last update date Oct 17, 2014
Contact name Takahiro Narimatsu
Organization name Oita University
Department Medicine
Lab Molecular Pathology
Street address Hasamamachi Idaigaoka 1-1
City Yufu
State/province Oita
ZIP/Postal code 8795503
Country Japan
 
Platform ID GPL8841
Series (1)
GSE43477 Genomic profiling of primary and metastatic clear cell renal cell carcinoma by array-based comparative genomic hybridization.

Data table header descriptions
ID_REF
VALUE log2 normalized ratio tumor/normal

Data table
ID_REF VALUE
A_14_P112718 0.13965757
A_14_P201353 -0.53595537
A_14_P108353 -0.41561186
A_14_P129881 -0.24878941
A_14_P114030 -0.54109263
A_14_P139527 0.16185208
A_14_P118340 0.08478184
A_14_P106890 -0.22400805
A_14_P122641 0.16350497
A_14_P107170 -0.06815996
A_14_P100766 0.41908735
A_14_P118104 0.17636351
A_14_P117253 -0.267179
A_14_P129407 -0.2021068
A_14_P200001 -0.26440108
A_14_P103811 -0.080053136
A_14_P119666 0.31368053
A_14_P100799 0.4345261
A_14_P121179 0.5542213
A_14_P115318 -0.4420141

Total number of rows: 42416

Table truncated, full table size 1013 Kbytes.




Supplementary file Size Download File type/resource
GSM1063437_M2P_FEATURE_EXTRACTION_v.9.1.3.1_Protocol_CGH-v4_91.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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