|
Status |
Public on Jan 19, 2018 |
Title |
HCC008_tumor tissue_SNP |
Sample type |
genomic |
|
|
Source name |
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).
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|
|
Hybridization protocol |
As per manufacturer (Affymetrix)
|
Scan protocol |
As per manufacturer (Affymetrix)
|
Description |
HCC008T
|
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
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|
|
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 |
|