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Sample GSM2040581 Query DataSets for GSM2040581
Status Public on Dec 27, 2016
Title Primary Tumor vs matched normal blood_Cervical cancer patient_#4253
Sample type genomic
 
Channel 1
Source name Primary tumor_#4253
Organism Homo sapiens
Characteristics subject status: Indian CACX (cancer of the uterine cervix) patient
subject id: #4253
Stage: Stage IIIB
age: 38
gender: F
tissue/cell type: Primary uterine cervical lesions
hpv type: HPV16,18
Growth protocol Primary uterine cervical lesions and corresponding peripheral blood lymphocytes (PBL) were collected from the hospital section of Chittaranjan National Cancer Institute, Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients were taken.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from cryosections (5µm) of tumor tissue specimen and PBL were isolated by standard phenol/chloroform method.
Label Treated_Cy5
Label protocol Agilent Direct method has been used for the sample processing. About 1000 ng of control and test DNA was used for the restriction digestion in the master mix containing AluI and RsaI restriction enzymes as per manufactures recommendation. The samples were incubated at 37°C for 2 hours followed by heat inactivation of enzymes at 65°C for 20 minutes. To confirm the efficiency of restriction enzymes to obtain fragments of size 200-500bp, about 2 μL of the digested gDNA was tested on a 0.8% agarose gel. Labeling of samples was done by random priming method, in which the random hexamers, Cy3-dUTP & Cy5-dUTP, dNTP, Buffer and Klenow enzyme was used. Briefly, 1X Random primer mix was added to each of 26µl digested control and test samples. The DNA was denatured at 95 °C for 3 minutes followed by snap chill on ice for 5 minutes. Master mix for Cy3 and Cy5 dNTPs was done separately to ensure that, the control sample is labeled with Cy3 and test sample with Cy5 respectively. About 19 ul of labeling master mix prepared as per manufacturers recommendation was added to the denatured control and test DNA sample and incubated at 37°C for 2 hours followed by enzyme heat inactivation at 65°C for 10 minutes. The labeled samples were cleaned up by Amicon 30kDa filter size exclusion filter.
 
Channel 2
Source name matched normal blood_#4253
Organism Homo sapiens
Characteristics subject status: Indian CACX (cancer of the uterine cervix) patient
subject id: #4253
tissue/cell type: corresponding peripheral blood lymphocytes (PBL)
Stage: Stage IIIB
age (yrs): 38
gender: F
Growth protocol Primary uterine cervical lesions and corresponding peripheral blood lymphocytes (PBL) were collected from the hospital section of Chittaranjan National Cancer Institute, Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients were taken.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from cryosections (5µm) of tumor tissue specimen and PBL were isolated by standard phenol/chloroform method.
Label Normal_Cy3
Label protocol Agilent Direct method has been used for the sample processing. About 1000 ng of control and test DNA was used for the restriction digestion in the master mix containing AluI and RsaI restriction enzymes as per manufactures recommendation. The samples were incubated at 37°C for 2 hours followed by heat inactivation of enzymes at 65°C for 20 minutes. To confirm the efficiency of restriction enzymes to obtain fragments of size 200-500bp, about 2 μL of the digested gDNA was tested on a 0.8% agarose gel. Labeling of samples was done by random priming method, in which the random hexamers, Cy3-dUTP & Cy5-dUTP, dNTP, Buffer and Klenow enzyme was used. Briefly, 1X Random primer mix was added to each of 26µl digested control and test samples. The DNA was denatured at 95 °C for 3 minutes followed by snap chill on ice for 5 minutes. Master mix for Cy3 and Cy5 dNTPs was done separately to ensure that, the control sample is labeled with Cy3 and test sample with Cy5 respectively. About 19 ul of labeling master mix prepared as per manufacturers recommendation was added to the denatured control and test DNA sample and incubated at 37°C for 2 hours followed by enzyme heat inactivation at 65°C for 10 minutes. The labeled samples were cleaned up by Amicon 30kDa filter size exclusion filter.
 
 
Hybridization protocol Equal amount of labeled Test & Control DNA sample was added into a fresh tube containing 25 µl of Human Cot-1 DNA (1mg/ml), 26ul of Agilent 10X blocking agent and 130ul Agilent 2X hybridization buffer. The total hybridization volume was 45ul. The above hybridization mix was denatured at 95°C for 3 minutes and incubated the microfuge tubes at 37°C for 30 minutes. The samples were hybridized at 65°C for 40 hours in the hybridization chamber. After hybridization, the slides were washed using aCGH Wash Buffer1 (Agilent Technologies, Part Number 5188-5221) at room temperature for 5 minutes and aCGH Wash Buffer 2 (Agilent Technologies, Part Number 5188-5222) at 37°C for 1 minutes. The slides were then washed with Acetonitrile for 10 seconds.
Scan protocol Agilent Scanner (Agilent Technologies, Part Number G2565CA).
Description Primary Tumor vs matched normal blood_Cervical cancer patient_#4253
1T_Cy5 vs. 1N_Cy3
Data processing Images were quantified using Agilent Feature Extraction Software . Feature extracted raw data was normalized using Lowes normalization and analyzed Agilent CytoGenomics 2.7 SoftwarE.
 
Submission date Jan 15, 2016
Last update date Dec 27, 2016
Contact name Susanta Roychoudhury
E-mail(s) anirbanr91@gmail.com
Organization name Saroj Gupta Cancer Centre & Research Institute
Street address Mahatma Gandhi Road, Thakurpukur
City Kolkata
State/province West Bengal
ZIP/Postal code 700063
Country India
 
Platform ID GPL11363
Series (1)
GSE76911 Catalogue of genomic alterations in uterine cervical carcinoma of Indian patients.

Data table header descriptions
ID_REF
VALUE normalized log2 ratio representing test/reference

Data table
ID_REF VALUE
A_14_P100000 0.06
A_14_P100002 -0.12
A_14_P100003 0.11
A_14_P100004 -0.11
A_14_P100005 -0.03
A_14_P100006 -0.02
A_14_P100008 -0.01
A_14_P100009 0.00
A_14_P100012 0.00
A_14_P100015 0.11
A_14_P100019 -0.01
A_14_P100024 0.01
A_14_P100025 0.15
A_14_P100026 0.16
A_14_P100028 0.00
A_14_P100029 0.04
A_14_P100031 0.00
A_14_P100036 0.10
A_14_P100041 0.03
A_14_P100043 -0.01

Total number of rows: 411052

Table truncated, full table size 8206 Kbytes.




Supplementary file Size Download File type/resource
GSM2040581_SG13134300_252808111286_S001_CGH_1105_Oct12_1_1.txt.gz 112.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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