|
| Status |
Public on May 09, 2016 |
| Title |
EC1475B |
| Sample type |
genomic |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
disease state: control
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
blood DNA was extracted and purified using standard phenol/chloroform method and tumor DNA was extracted using Purification Tissue Kit (Centra System.)
|
| Label |
biotin
|
| Label protocol |
As per manufacturer protocol (Affymetrix)
|
| |
|
| Hybridization protocol |
fragmentation is confirmed by the presence of a smear between 50 to 200bp, the sample was end labeled with biotin and hybridized onto the array. The chip was incubated at 49oC for 18 hours in the Affymetrix Genechip system hybridization oven
|
| Scan protocol |
The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Hybridized to SNP5.0
|
| Data processing |
Raw GenomeWideSNP_5 CEL files were pre-processed using PennCNV [Wang K, 2007]. This protocol extracts allele-specific signal intensities from genotyping arrays, and then integrates information on SNP spacing and SNP allele frequencies to generate CNV calls by a hidden Markov model (HMM) algorithm.
PennCNV-Affy is a data-preprocessing protocol for Affymetrix genome-wide 5.0. The protocol converts raw CEL files into a signal intensity file that contains Log R Ratio (LRR) and B Allele Frequency (BAF) values.
CNV data can be calculated from LRR (2*2^LRR).
|
| |
|
| Submission date |
Jan 14, 2013 |
| Last update date |
May 09, 2016 |
| 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 |
GPL6804 |
| Series (1) |
| GSE43470 |
Genomic landscape of somatic alterations in esophageal squamous cell carcinoma and gastric cancer |
|
