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Sample GSM2267447 Query DataSets for GSM2267447
Status Public on Sep 28, 2016
Title N20021007 [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

Supplementary file Size Download File type/resource
GSM2267447_20021007N_V6.CEL.gz 28.9 Mb (ftp)(http) CEL
Processed data not provided for this record

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