|
Status |
Public on Feb 26, 2015 |
Title |
NASH [0661_SEN_252185018607_S01_CGH_107_Sep09_1_2] |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
NAFLD
|
Organism |
Homo sapiens |
Characteristics |
Stage: NASH blood: lymphocytes age: 60s gender: Female
|
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: 60s gender: Female
|
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 |
|