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Sample GSM2267443 Query DataSets for GSM2267443
Status Public on Sep 28, 2016
Title T2001206 [SNP]
Sample type genomic
 
Source name Gastric Primary Tissue
Organism Homo sapiens
Characteristics tissuetype: Gastric primary tumor tissue
histology: diffuse
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 copy number altered regions followed by the copy number alteration status
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
GSM2267443_AFCT1163-57.CEL.gz 33.6 Mb (ftp)(http) CEL
GSM2267443_P2001206_cna.bed.gz 7.4 Kb (ftp)(http) BED
Processed data provided as supplementary file

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