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Sample GSM1588653 Query DataSets for GSM1588653
Status Public on Jan 22, 2016
Title Invasive region of IPMN-inv (Case 30)
Sample type genomic
 
Channel 1
Source name IPMN : FFPE sample
Organism Homo sapiens
Characteristics gender: female
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 mixed genomic DNA of normal renal cortex : FFPE sample
Organism Homo sapiens
Characteristics gender: 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 65℃ for 40 h
Scan protocol A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm
Description Genomic DNA was extracted from tissues of normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma, neither of which exhibited invasion or metastasis to the renal cortex. The same amount of genomic DNA extracted from 12 patients was mixed and used as the control DNA.
Data processing Microarray images were analyzed using FEATURE EXTRACTION v. 9.1 (Agilent Technologies) with linear normalization protocol CGH-v4_91 (Case 1-12) or CGH-v4_95_Feb07 (Case 14, 16-20, 22-31 and 40), and the resulting data were imported into DNA Analytics v. 3.4 (Agilent Technologies). After normalization of the raw data, the log2ratio of Cy5 (cancer) to Cy3 (control) was calculated. Next, aberrant regions were determined using the ADM-2 algorithm at a threshold of 8.0. To detect gains and losses, we set the values of parameters for the aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.3, maximum number of aberrant regions 10,000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2 ratio at 0.3 to detect regions showing a change in the averaged copy number of more than 1.23-fold (log2(1.23) = 0.3).
 
Submission date Jan 22, 2015
Last update date Jan 22, 2016
Contact name Naoki Hijiya
E-mail(s) hijiya@oita-u.ac.jp
Phone 1975865693
Organization name Oita University
Department Medicine
Lab Molecular pathology
Street address 1-1, Idaigaoka Hasama-machi
City Yufu
State/province Oita
ZIP/Postal code 879-5593
Country Japan
 
Platform ID GPL9128
Series (1)
GSE65181 Genomic profiling of IPMN with an associated invasive carcinomas (IPMN-inv) and invasive ductal carcinomas (IDC) by array-based comparative genomic hybridization

Data table header descriptions
ID_REF
VALUE the log2ratio of Cy5 (cancer) to Cy3 (control)

Data table
ID_REF VALUE
A_14_P112718 -0.44988367
A_16_P15000916 -0.65301204
A_16_P15001074 0.58777463
A_16_P00000012 -0.4885824
A_16_P00000014 0.10545211
A_16_P00000017 0.20230073
A_16_P00000021 0.77603024
A_16_P00000023 0.9579654
A_16_P00000027 0.55769765
A_16_P00000033 -0.08174219
A_16_P35001586 0.11084533
A_16_P15001533 -0.042510502
A_16_P00000060 -0.33714193
A_16_P15001594 0.6136861
A_16_P00000082 1.3711883
A_16_P00000090 0.74931365
A_16_P00000099 0.13991433
A_16_P15001666 0.5349188
A_16_P00000112 1.3834921
A_16_P00000114 1.0904549

Total number of rows: 235829

Table truncated, full table size 5928 Kbytes.




Supplementary file Size Download File type/resource
GSM1588653_P30-Ca-0800_S01_CGH-v4_95_Feb07.txt.gz 23.5 Mb (ftp)(http) TXT
Processed data are available on Series record
Processed data included within Sample table

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