|
| Status |
Public on Sep 28, 2016 |
| Title |
N2001206 [SNP] |
| Sample type |
genomic |
| |
|
| Source name |
Gastric Primary Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissuetype: Gastric primary non-malignant tissue
histology: not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.
|
| 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 Gene Chip Scanner 3000.
|
| Description |
The SNP6 profile of this sample was used to generate the reference model for normalizing the following cancer profiles: T2000639, T990068, T2000877. The normalized cancer profiles were subsequently used to detect copy number changes, reported in P2000639_cna.bed, P990068_cna.bed and P2000877_cna.bed, respectively.
|
| Data processing |
Data in .CEL format was processed in the following order (Deng et. al., 2012): (1) Normalization: Raw .CEL files were processed using Affymetrix Genotyping Console 4.2. Reference models were created from SNP6.0 profiles of normal gastric tissues according to the hybridization batch. Copy number changes in cell lines and primary tumor samples were determined by using the reference model from primary normal samples. (2) Segmentation: Copy number segmentation data was produced using the circular binary segmentation (CBS) algorithm implemented in the DNAcopy R package.
copy number altered regions followed by the copy number alteration status
|
| |
|
| Submission date |
Aug 11, 2016 |
| Last update date |
Sep 28, 2016 |
| Contact name |
Aditi Qamra |
| E-mail(s) |
qamraa99@gis.a-star.edu.sg
|
| Organization name |
GIS
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE85466 |
Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [SNP] |
| GSE85467 |
Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity |
|
