|
| Status |
Public on Jul 25, 2012 |
| Title |
Asian sample no.136 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
disease status: non-small cell lung cancer (NSLCL)
race: Asian
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA was prepared using proteinase K digestion and phenol-chloroform extraction.
|
| Label |
Cy5
|
| Label protocol |
500 ng of tumor genomic DNA and reference DNA (for Asian samples: 28 matched-normal genomic DNA pool; for Caucasian samples: commercial human genomic DNA, Invitrogen) were labeled by random priming using BioPrime DNA Labeling System (Invitrogen) with Cy3-dCTP (tumor) or Cy5-dCTP (reference).
|
| |
|
| Channel 2 |
| Source name |
Reference sample
|
| Organism |
Homo sapiens |
| Characteristics |
reference source: 28 matched-normal genomic DNA pool from Aaian lung cancer
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA was prepared using proteinase K digestion and phenol-chloroform extraction.
|
| Label |
Cy3
|
| Label protocol |
500 ng of tumor genomic DNA and reference DNA (for Asian samples: 28 matched-normal genomic DNA pool; for Caucasian samples: commercial human genomic DNA, Invitrogen) were labeled by random priming using BioPrime DNA Labeling System (Invitrogen) with Cy3-dCTP (tumor) or Cy5-dCTP (reference).
|
| |
|
| |
| Hybridization protocol |
Labeled tumor and reference DNA were combined together with 100 μg human Cot-1 DNA (Invitrogen). Hybridization was performed using MAUI hybridization system (BioMcro Systems, Salt Lake City, UT), agitating the hybridization solution for 50 hours at 50℃.
|
| Scan protocol |
The arrays were scanned using scanner GenePix4000B (Axon Instruments, Foster City, CA) and the images were segmented and transformed to Cy3-Cy5 log ratio using GenePix software by Axon Instruments, Inc. (http://www.axon.com).
|
| Description |
Asian lung cancer sample 36
|
| Data processing |
Further data processing, a normalization method called “block-wise normalization”, which normalized the array-CGH data by the log ratio of the self-self hybridization of reference DNA according to the mean and the standard deviations of each array block, was established.
|
| |
|
| Submission date |
Apr 09, 2010 |
| Last update date |
Jul 25, 2012 |
| Contact name |
Yi-Ching Wang |
| E-mail(s) |
[email protected]
|
| Phone |
+886-6-2353535
|
| Organization name |
National Cheng Kung University
|
| Department |
Department of Pharmacology, College of Medicine
|
| Street address |
No.1, University Road, Tainan 70101, Taiwan, R. O. C.
|
| City |
Tainan |
| ZIP/Postal code |
70101 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL10303 |
| Series (1) |
| GSE21276 |
Novel Lung Cancer-Related Genes Identified by a Non-Gapped Array-Comparative Genomic Hybridization Microarray in Asian and Caucasian Populations |
|
