|
| Status |
Public on Aug 17, 2010 |
| Title |
Lung metastatic cell line generation 2 in RCC, biological rep 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human RCC cell line LM2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LM2
metastasis: Metastatic
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA was performed using Qiagen DNeasy kit according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
genomic DNA samples were labeled using the BioPrime Array CGH Labeling kit (Invitrogen catalog #18095-012) according to the manufacturer's protocol, except 10μg of amplified DNA was used in each reaction instead of 4μg.
|
| |
|
| Channel 2 |
| Source name |
Promega reference human genome DNA from normal male
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Promega reference human genome DNA from normal male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA was performed using Qiagen DNeasy kit according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
genomic DNA samples were labeled using the BioPrime Array CGH Labeling kit (Invitrogen catalog #18095-012) according to the manufacturer's protocol, except 10μg of amplified DNA was used in each reaction instead of 4μg.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent Technologies Scanner G2505B US45103030.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
LM2 metastatic RCC cell line as experimental DNA, biological rep1 and Promega reference DNA as control
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Aug 14, 2010 |
| Last update date |
Aug 16, 2010 |
| Contact name |
Venkata J Thodima |
| E-mail(s) |
tvjagan@gmail.com
|
| Phone |
2126393595
|
| Fax |
2127173541
|
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Department |
Cell Biology
|
| Lab |
Chaganti
|
| Street address |
430 E 67th St RRL#337
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL4091 |
| Series (2) |
| GSE23631 |
RCC cell lines and paired tumors |
| GSE23633 |
Array comparative genomic hybridization data from RCC cell lines to study metastasis progression |
|
