|
| Status |
Public on Dec 31, 2018 |
| Title |
NCI-H716_Genome-wide_400K_CGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human colorectal cancer cell line NCI-H716
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal adenocarcinoma
cell line: NCI-H716
cell type: cancer cell line
gender: male
|
| Growth protocol |
The cells were cultured in RPMI1640 medium (Gibco, Carlsbad, CA, US) supplemented with 10% fetal bovine serum (Gibco, Carlsbad, CA, US) in a humidified atmosphere of 5% CO2 at 37°C. Cells were authenticated by short tandem repeat profiling analysis (Beijing Microread Genetics, Beijing, China).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
Tumor and control DNA were labeled by random priming with Cy5- and Cy3-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
Commercial Male DNA reference from Agilent
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
gender: male
|
| Growth protocol |
The cells were cultured in RPMI1640 medium (Gibco, Carlsbad, CA, US) supplemented with 10% fetal bovine serum (Gibco, Carlsbad, CA, US) in a humidified atmosphere of 5% CO2 at 37°C. Cells were authenticated by short tandem repeat profiling analysis (Beijing Microread Genetics, Beijing, China).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Tumor and control DNA were labeled by random priming with Cy5- and Cy3-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours.
|
| Scan protocol |
Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).
|
| Data processing |
The data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method (The z-score algorithm at threshold 4) - CGH v2 proposed by Agilent.
|
| |
|
| Submission date |
Feb 02, 2018 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Xueyuan Jia |
| E-mail(s) |
jiaxueyuan@126.com
|
| Organization name |
Harbin Medical University
|
| Lab |
Laboratory of Medical Genetics
|
| Street address |
157 Baojian Road, Nangang District
|
| City |
Harbin |
| ZIP/Postal code |
150081 |
| Country |
China |
| |
|
| Platform ID |
GPL19387 |
| Series (2) |
| GSE110069 |
Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [400K] |
| GSE110071 |
Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 |
|
