|
| Status |
Public on Mar 22, 2022 |
| Title |
ESCC E1628B |
| Sample type |
genomic |
| |
|
| Source name |
ESCC E1628B
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Esophageal squamous cell carcinoma (ESCC)
tissue: Blood
individual id: E1628
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Germline DNA from whole blood was extracted and purified using the standard phenol/chloroform method. DNA was extracted from tumor by using the Allprep kit (Qiagen). DNA quality and quantity were determined using NanoDrop 2000 (Thermo Scientific).
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 3000.
|
| Description |
ESCC E1628B
Hybridized to SNP6.0
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
Mar 21, 2019 |
| Last update date |
Mar 24, 2022 |
| Contact name |
Maxwell Lee |
| E-mail(s) |
leemax@mail.nih.gov
|
| Phone |
240-276-5239
|
| Organization name |
National Cancer Institute, NIH
|
| Department |
CCR
|
| Lab |
Laboratory of Human Carcinogenesis
|
| Street address |
Building 37, Room 5120
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE128695 |
An association study between somatic alterations and eQTL in immunity, DNA repair and inflammation pathways in esophageal squamous cell carcinoma (ESCC) |
|
