|
| Status |
Public on Jun 27, 2017 |
| Title |
CCA Tumor Tissue LCS_604A |
| Sample type |
genomic |
| |
|
| Source name |
CCA Tumor Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver Tumor Tissue
disease state: Cholangiocarcinoma (CCA)
sample name matched with transcriptome data: LCS_604A
individual: LCS_604
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from frozen tissue using Phenol/Chloroform extraction protocol. Samples with sufficient amount of double-stranded DNA as confirmed by Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) were included for array studies.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix procedures
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures
|
| Scan protocol |
Standard Affymetrix procedures using GeneChip Scanner 3000 uisng AGCC software
|
| Data processing |
PARTEK Genomic suite (6.6) was used to import allele intensity from the CEL files. Interrogating probes was imported without filtering probes. Adjusmentt for fragment length and probe sequence was performed using the Partek default option. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19). Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values were generated in Partek Genomics Suite (v 6.6) using a paired non-tumor sample as reference following the paired workflow.
Copy number ratio values of tumor sample using a paired non-tumor sample as reference (total 153 columns)
|
| |
|
| Submission date |
Dec 21, 2015 |
| Last update date |
Jun 27, 2017 |
| Contact name |
Xin Wei Wang |
| E-mail(s) |
xw3u@nih.gov
|
| Phone |
240-760-6858
|
| Organization name |
National Cancer Institute
|
| Department |
Laboratory of Human Carcinogenesis
|
| Lab |
Liver Carcinogenesis Unit
|
| Street address |
37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-4255 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE76213 |
Copy Number Variation of human hepatocellular carcinoma (HCC) and Cholangiocarcinoma (CCA) from the Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC) |
| GSE76311 |
Human hepatocellular carcinoma (HCC) and Cholangiocarcinoma (CCA) from Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC) |
|
