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Sample GSM1341024 Query DataSets for GSM1341024
Status Public on Feb 26, 2015
Title NASH [0599_SEN_252185017027_S01_CGH_107_Sep09_1_2]
Sample type genomic
 
Channel 1
Source name NAFLD
Organism Homo sapiens
Characteristics Stage: NASH
blood: lymphocytes
age: 30s
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were extracted using Qiagen as recommended by the manufacturer
Label Cy3
Label protocol Reaction tubes were prepared as a mixture of 18 μL of genomic DNA sample (or reference), 10 μL of random primer and 10 μL of reaction buffer. The reactions were mixed and centrifuged for 15 s, followed by denaturation in a PCR block with a heated lid at 99°C for 20 min. Immediately after, the tubes were placed on ice for 5 min. On ice, the followings were added to the tubes: 10 μL of dCTP labelling mix, 1 μL of Cy3-dCTP (for sample) / 1 μL of Cy5-dCTP (for reference), and 1 μL of Klenow. The mixture was centrifuged for 15 s and incubated at 37°C for 2 h. Following that, the mixture was incubated at 65°C for 10 min, then placed on ice for 5 min. The mixture was centrifuged for 15 s.
 
Channel 2
Source name Control
Organism Homo sapiens
Characteristics blood: lymphocytes
age: 30s
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were extracted using Qiagen as recommended by the manufacturer
Label Cy5
Label protocol Reaction tubes were prepared as a mixture of 18 μL of genomic DNA sample (or reference), 10 μL of random primer and 10 μL of reaction buffer. The reactions were mixed and centrifuged for 15 s, followed by denaturation in a PCR block with a heated lid at 99°C for 20 min. Immediately after, the tubes were placed on ice for 5 min. On ice, the followings were added to the tubes: 10 μL of dCTP labelling mix, 1 μL of Cy3-dCTP (for sample) / 1 μL of Cy5-dCTP (for reference), and 1 μL of Klenow. The mixture was centrifuged for 15 s and incubated at 37°C for 2 h. Following that, the mixture was incubated at 65°C for 10 min, then placed on ice for 5 min. The mixture was centrifuged for 15 s.
 
 
Hybridization protocol Hybridization mix was prepared. The target was denatured and the mixture was incubated. The Agilent SureHyb Gasket was placed into an Agilent Chamber base. Immediately, hybridisation mix was pipetted onto the gasket slide. OGT array was placed onto the Gasket slide. The hybridisation chamber was placed in the hybridisation oven and hybridised. After hybridization, slides were washed sequential.
Scan protocol Scanned on an Agilent G2565AA scanner.
Description Normalised ratios between patients and controls were used for CNV calls
Data processing Data were extracted using Feature Extraction Software (version 10.7.3.1) and uploaded into the CytoSure™ Interpret software (version 4.2.5), normalized and converted into .cgh files. The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm.
 
Submission date Mar 06, 2014
Last update date Feb 26, 2015
Contact name shamsul mohd zain
E-mail(s) soulz712@gmail.com
Organization name univeristy of malaya
Department department of pharmacology
Lab the pharmacogenomics laboratory
Street address jalan lembah pantai
City kuala lumpur
ZIP/Postal code 50603
Country Malaysia
 
Platform ID GPL9777
Series (1)
GSE55645 Genome wide analysis of copy number variation in NAFLD spectrum

Data table header descriptions
ID_REF
VALUE Log2 intensity ratios of sample to reference (Cy3/Cy5: log2-ratios above 0.3 for duplications and below -0.6 for deletions)

Data table
ID_REF VALUE
1 5.11E-02
2 0.00E+00
3 0.00E+00
4 -5.90E-02
5 9.64E-02
6 2.42E-01
7 -3.95E-02
8 1.39E-02
9 6.68E-03
10 3.52E-02
11 2.72E-02
12 -5.04E-02
13 5.26E-02
14 -1.01E-01
15 4.66E-03
16 -1.68E-02
17 2.90E-01
18 4.64E-01
19 -8.87E-03
20 8.98E-02

Total number of rows: 420288

Table truncated, full table size 6682 Kbytes.




Supplementary file Size Download File type/resource
GSM1341024_0599_SEN_252185017027_S01_CGH_107_Sep09_1_2.txt.gz 117.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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