|
| Status |
Public on Dec 04, 2020 |
| Title |
Fresh frozen metastatic tumor_4 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung cancer mestastatic brain tumor
gender: M
type: poorly diff squamous
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
EZ1 Advanced workstation and DNA Tissue Kit (Qiagen, Germantown, MD).
|
| Label |
Cy5
|
| Label protocol |
Cancer and reference DNA (500ng each) were labeled with fluorescent dyes, Cy5 and Cy3 respectively, using the SureTag Complete DNA Labeling Kit (Agilent Technologies)
|
| |
|
| Channel 2 |
| Source name |
normal human reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
reference source: Agilent catalog number 5190-3796
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
EZ1 Advanced workstation and DNA Tissue Kit (Qiagen, Germantown, MD).
|
| Label |
Cy3
|
| Label protocol |
Cancer and reference DNA (500ng each) were labeled with fluorescent dyes, Cy5 and Cy3 respectively, using the SureTag Complete DNA Labeling Kit (Agilent Technologies)
|
| |
|
| |
| Hybridization protocol |
Genome-wide copy number variation was measured by a 2-color microarray approach using Agilent SurePrint G3 ISCA Human Cancer CGH+SNP 180K x 4 arrays
|
| Scan protocol |
CytoCGH_0205_Oct12 protocol and Agilent G4900DA SureScan Microarray Scanner System
|
| Data processing |
Probe fluorescence intensity data was extracted from scanned microarray images using Agilent Cytogenomics software Edition 2.5.8.1. GC Correction, Diploid Peak Centralization (normalization) and Aberration Detection Method 2 (quality control) algorithms were also applied using this software. Aggregate data (all 27 samples) were further analyzed using NEXUS Copy Number software (Biodiscovery) to identify recurring genomic aberrations.
Feature extraction files for each sample and data matrix contain the normalized log10 Cy5/Cy3 values for each probe, results of aggregate data analysis by NEXUS Copy Number software include frequency and chromosome region of common aberrations
|
| |
|
| Submission date |
Sep 04, 2020 |
| Last update date |
Dec 04, 2020 |
| Contact name |
Aliccia Bollig-Fischer |
| E-mail(s) |
bollig@karmanos.org
|
| Organization name |
Karmanos Cancer Institute & Wayne State University
|
| Department |
Oncology
|
| Street address |
4100 John R
|
| City |
Detroit |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL16237 |
| Series (1) |
| GSE157515 |
Array comparative genomic hybridization analysis of metastatic lung tumors |
|
