|
| Status |
Public on Jan 19, 2018 |
| Title |
HCC008_non-tumor tissue_SNP |
| Sample type |
genomic |
| |
|
| Source name |
adjacent non-tumor liver tissues of HCC patient
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: HCC008
subject status: hepatocellular carcinoma (HCC) patient
gender: male
age: 39
tnm staging: T2N0M0
|
| Treatment protocol |
For all tumors and non-tumor tissues, samples were snap frozen and stored at -80°C. Tumor sections had to contain more than 70% tumor cell nuclei and less than 20% necrosis in all tumor samples.
|
| Growth protocol |
none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from frozen tissues using proteinase K digestion and subsequent phenol/chlororform extraction. DNA concentration and purity were determined using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, USA).
|
| Label |
Biotin
|
| Label protocol |
DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by an Affymetrix service facility (CapitalBio Corporation, China).
|
| |
|
| Hybridization protocol |
As per manufacturer (Affymetrix)
|
| Scan protocol |
As per manufacturer (Affymetrix)
|
| Description |
HCC008N
|
| Data processing |
From raw.CEL file, Copy-number estimation using Robust Multichip Analysis (CRMA) was used to pre-process the probe signal intensities. The procedure included that signal intensities were calibrated for offset and crosstalk between alleles, and normalized for probe sequence effects. After summarizing to probe-set level signals, fragment-length effects were normalized. Next, raw copy numbers was calculated by paired analysis, taking paired tumor-adjacent tissue as a reference for every tumor tissue. Then segmented copy number profiles were analyzed using Circular binary segmentation (CBS) algorithm2 with default parameters in the R package “DNA-copy” (http://www.r-project.org/).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
Jan 18, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Gangqiao Zhou |
| E-mail(s) |
zhougq114@126.com
|
| Organization name |
Beijing Institute of Radiation Medicine
|
| Street address |
No. 27, Taiping Road, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE109360 |
Integrative genomic analysis in HCC samples [SNP] |
| GSE109361 |
Integrative genomic analysis in HCC samples |
|
