|
| Status |
Public on Jun 09, 2017 |
| Title |
26a |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
primary liver tumor
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 26
patient gender: male
patient age at resection: 20.2
tissue: primary liver tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from FFPE samples was extracted using the Agilent protocol for oligonucleotide array-based CGH for genomic DNA analysis. DNA integrity was verified on a 1% agarose gel.
|
| Label |
Cy5
|
| Label protocol |
3 mg of DNA was then heat-fragmented and labeled with the ULS Labeling V3.4 kit, according to the manufacturer’s instructions (Agilent).
|
| |
|
| Channel 2 |
| Source name |
Roche Human Genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
reference dna info.: Roche catalog. 11691112001
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from FFPE samples was extracted using the Agilent protocol for oligonucleotide array-based CGH for genomic DNA analysis. DNA integrity was verified on a 1% agarose gel.
|
| Label |
Cy3
|
| Label protocol |
3 mg of DNA was then heat-fragmented and labeled with the ULS Labeling V3.4 kit, according to the manufacturer’s instructions (Agilent).
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was hybridized to Agilent 1M CGH arrays for 40 hours at 60°C.
|
| Scan protocol |
After washing, the slides were scanned and images quantified using Feature Extraction 9.1 (Agilent).
|
| Description |
MC_02_18448_slide098_S01_CGH_107_Sep09
|
| Data processing |
The aCGH data were first processed using a normalization procedure to correct for block, row, column or intensity effects as well as any artifact such as dependence of log-ratios on the genomic GC content. The normalized data were then segmented using the Circular Binary Segmentation algorithm (CBS) to compute copy number regions and alterations. The RAE method is then used to analyze cohort-wide CNAs in the tumor samples and assigns a copy number status (diploid, gain, loss) to all contiguous regions in each sample of the genome [Taylor BS, Barretina J, Socci ND, Decarolis P, Ladanyi M, Meyerson M, Singer S, Sander C. Functional copy-number alterations in cancer. PLoS One 2008;3:e3179.] The 'GeneMatrix.txt' is obtained by assigning a copy number status to genes in the regions.
The sample data table contains normalized data included in the LogRatio column (in *GCNormV4b.txt file). The normalized data were generated using both the genomic artificial models and lowess normalization method, which are described at http://cbio.mskcc.org/CGCC/
|
| |
|
| Submission date |
Dec 11, 2014 |
| Last update date |
Jun 09, 2017 |
| Contact name |
Jeffrey Zhao |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Genomics Core
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL8736 |
| Series (1) |
| GSE64103 |
Genome profiling of fibrolamellar carcinoma [CGH] |
|
