tissue: head and neck squamous cell carcinoma tumor site: oral tumor id: 106
Treatment protocol
None.
Growth protocol
Fresh-frozen human tissue.
Extracted molecule
genomic DNA
Extraction protocol
Qiagen Qiamp DNA extraction kit.
Label
biotin
Label protocol
As per manufacturer (Affymetrix).
Hybridization protocol
As per manufacturer (Affymetrix).
Scan protocol
As per manufacturer (Affymetrix).
Description
Tumor ID 106 Hybridized to 250K_Nsp.
Data processing
Data were collected at the Harvard Partners Microarray Core Facility. Inferred copy number states of each SNP were extracted and converted from .CEL files into signal intensities using GCOS and Affymetrix Copy Number Analysis Tool (CNAT) v4.0.1. We utilized the HMM-based algorithm with defaults for tuning parameters, Gaussian smoothing, transition decay, and median scaling.
The 'GSE20939_tumor_copy_number.txt' file, which is linked to the Series GSE20939 record as a supplementary file, contains the (blood-adjusted) tumor copy number calls used in our final analyses.
Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted (Affymetrix Copy Number)
Data table header descriptions
ID_REF
VALUE
Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1
Relative allele signal for the data in the first probe group
RAS2
Relative allele signal for the data in the second probe group