|
| Status |
Public on Feb 28, 2013 |
| Title |
Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human Esophageal Squamous Cell Carcinoma Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human Esophageal Squamous Cell Carcinoma
age: 64
Sex: Male
location: Esophagus
|
| Growth protocol |
Each cell line was cultured in RPMI-1640 (Invitrogen) supplemented with 10% fetal calf serum at 37℃ with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
1 μg the reference commercial genomic DNA (promega) and the same amount of the test (cell line) DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
|
| Label |
Cy3
|
| Label protocol |
The digested test and reference DNA fragments were labeled with Cy3-dUTP and Cy5-dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449), respectively. Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.
|
| |
|
| Channel 2 |
| Source name |
Commercial Human Genomic DNA: Male
|
| Organism |
Homo sapiens |
| Characteristics |
company: Promega
catalog: G1471
|
| Growth protocol |
Each cell line was cultured in RPMI-1640 (Invitrogen) supplemented with 10% fetal calf serum at 37℃ with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
1 μg the reference commercial genomic DNA (promega) and the same amount of the test (cell line) DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
|
| Label |
Cy5
|
| Label protocol |
The digested test and reference DNA fragments were labeled with Cy3-dUTP and Cy5-dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449), respectively. Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.
|
| |
|
| |
| Hybridization protocol |
Reference DNA probes and test DNA probes were combined and Human Cot-1 DNA (Invitrogen), 10 Blocking Agent and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, then samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.
|
| Scan protocol |
Scanned on an Agilent G2565B Scanner
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
|
| Description |
KYSE30
Biological replicate 1 of 6.Human Esophageal squamous cell carcinoma cell line
|
| Data processing |
Agilent Feature Extraction Software (version 9.1.3.1) was used for background subtraction and Linear normalization.
Agilent Genomic Workbench Lite Edition 5.0 use centralization algorithm to normalize the data of arrays and use ADM-2 algorithm to analyze the aberration data.
|
| |
|
| Submission date |
Feb 27, 2012 |
| Last update date |
Feb 28, 2013 |
| Contact name |
Jia-Jie Hao |
| E-mail(s) |
haojj2011@gmail.com
|
| Organization name |
Cancer Hospital (Institute), Chinese Academy of Medical Sciences
|
| Lab |
State Key Laborary of Molecular Oncology
|
| Street address |
17 Panjiayuan Nanli
|
| City |
Beijing |
| ZIP/Postal code |
100021 |
| Country |
China |
| |
|
| Platform ID |
GPL5477 |
| Series (1) |
| GSE36115 |
Genomic copy number alterations in human esophageal squamous cell carcinoma (ESCC) cell lines |
|
