|
| Status |
Public on Dec 31, 2014 |
| Title |
fresh frozen metastatic tumor_6 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
12-16
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer metastasis brain tumor
|
| Treatment protocol |
tumor specimens were either FFPE or fresh frozen as indicated in the sample list
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the EZ1 Advanced XL magnetic bead technology, the EZ1 DNA de-paraffinization method (where appropriate) and the EZ1 DNA Tissue kit (Qiagen, Valencia, CA). DNA was analyzed for quantity by nanodrop 3000 () and quality using the TapeStation (Agilent Technologies, Santa Clara, CA).
|
| 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) or Universal Linkage System labeling kit for DNA from FFPE specimens
|
| |
|
| Channel 2 |
| Source name |
Female Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference tissue: Agilent Female European DNA
|
| Treatment protocol |
tumor specimens were either FFPE or fresh frozen as indicated in the sample list
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the EZ1 Advanced XL magnetic bead technology, the EZ1 DNA de-paraffinization method (where appropriate) and the EZ1 DNA Tissue kit (Qiagen, Valencia, CA). DNA was analyzed for quantity by nanodrop 3000 () and quality using the TapeStation (Agilent Technologies, Santa Clara, CA).
|
| 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) or Universal Linkage System labeling kit for DNA from FFPE specimens
|
| |
|
| |
| 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 |
Raw data files were acquired using software: Agilent Feature Extraction for Cytogenomics 2.5.1.0. Sample Tables contain the log10 Cy5/Cy3 from the Feature Extraction File. Log2 ratios for genome (hg19) coordinates and genes showing copy number variation (CNV) were acquired using Agilent CytoGenomics Edition 2.5.8.1 using the CGH_v2 default, the ADM2 threshold set at 6 and an 8 probe minimum. An additional absolute log2 ratio threshold was set at 0.4 for analysis of reoccurring lesions or 0.8 to study high amplitude copy number aberrations. The sample supplementary files named "IntervalBasedReport*.txt" contain the genomic coordinates and genes displaying CNV.
|
| |
|
| Submission date |
Oct 02, 2014 |
| Last update date |
Dec 31, 2014 |
| 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) |
| GSE62009 |
Cytogenomic profiling of breast cancer brain metastases reveals potential for repurposing targeted therapeutics |
|
