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Sample GSM587483 Query DataSets for GSM587483
Status Public on Mar 11, 2011
Title Patient_OC1647
Sample type genomic
 
Channel 1
Source name Pooled Genomic DNA Male
Organism Homo sapiens
Characteristics gender: Male
cell type: Peripheral Blood Lymphocytes
sample type: Pooled Genomic DNA Male
Treatment protocol Freshly collected oral tissues from oral cancer patients and peripheral blood lymhocytes from healthy donors were kept at -80°C till DNA was extracted.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by standard phenol chloroform method. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.
Label Cy3
Label protocol The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 1 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.
 
Channel 2
Source name Oral Tumor Tissue
Organism Homo sapiens
Characteristics tissue: Oral Tumor
age: 48y
gender: Male
site: Gingivobuccal complex
Stage: 4
Treatment protocol Freshly collected oral tissues from oral cancer patients and peripheral blood lymhocytes from healthy donors were kept at -80°C till DNA was extracted.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by standard phenol chloroform method. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.
Label Cy5
Label protocol The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 1 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.
 
 
Hybridization protocol 5 micrograms of cy3 and cy5 labeled samples were hybridized. Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 40 hours
Scan protocol The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C
Description Biological replicate
Data processing The Analysis was done using Agilent DNA Analytics Software. Significant abberations were identified. (CY5 Treated vs. Cy3 Control)
 
Submission date Aug 26, 2010
Last update date Aug 03, 2012
Contact name Manoj Balkrishna Mahimkar
E-mail(s) mmahimkar@actrec.gov.in
Phone +91-22-27405049
Organization name Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre
Lab Mahimkar Lab
Street address Sector-22, Owe Village, Kharghar Node
City Navi Mumbai
State/province Maharashtra
ZIP/Postal code 410208
Country India
 
Platform ID GPL10722
Series (1)
GSE23831 Array CGH analysis of Oral Squamous Cell Carcinoma

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 test/reference

Data table
ID_REF VALUE
1 0.061586589
2 0
3 0
4 -0.098905671
5 -0.161046352
6 -0.300659
7 0.130470001
8 0.280027563
9 0.407882604
10 0.169937573
11 0.275666604
12 0.03123926
13 -0.05739351
14 -0.1060679
15 0.073038303
16 0.144694263
17 0.078662098
18 -0.154086197
19 -0.427715599
20 0.035315292

Total number of rows: 104702

Table truncated, full table size 1866 Kbytes.




Supplementary file Size Download File type/resource
GSM587483_US83000164_252176410017_S01_CGH_105_Dec08_1_1.txt.gz 29.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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