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Sample GSM1815840 Query DataSets for GSM1815840
Status Public on Mar 03, 2016
Title T065
Sample type genomic
Source name Type II Enteropathy-associated T-cell lymphoma Sample T065
Organism Homo sapiens
Characteristics tissue type: Tumor tissue
disease state: Type II Enteropathy-associated T-cell lymphoma
Treatment protocol NA
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from snap frozen patient specimens and whole blood was extracted using Blood & Cell Culture DNA Kit (Qiagen)
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 Hybridized to SNP6 array
raw B-allele frequency value; 'LRR' = normalized logR value; 'normalized_BAF' = normalized B-allele frequency (after TumorBoost); 'nA' = copy number of allele A; 'nB' = copy number of allele B (for the matche normal tissue only the raw BAF value is provided, as this is the only information necessary for processing the tumor using TumorBoost and ASCAT)
Data processing The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched normal CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.
Submission date Jul 08, 2015
Last update date Mar 03, 2016
Contact name Sanjanaa Nagarajan
Organization name National Cancer Centre Singapore
Department Department of Medical Sciences
Lab NCCS-VARI Translational Research Laboratory
Street address 11 Hospital Drive
City Singapore
State/province Singapore
ZIP/Postal code 169610
Country Singapore
Platform ID GPL6801
Series (2)
GSE70653 Affymetrix Genome-Wide Human SNP Array 6.0 data for Type II Enteropathy-associated T-cell lymphoma
GSE70654 Type II Enteropathy-associated T-cell lymphoma

Data table header descriptions
VALUE LRR = normalized logR value

Data table
ID_REF VALUE normalized_BAF nA nB
SNP_A-8575125 0.577866653 0.003161352 1 1
SNP_A-8575115 0.281937753 1.015937328 1 1
SNP_A-8575371 -0.21033199 1.025448561 1 1
SNP_A-8709646 -0.17726968 -0.015410423 1 1
SNP_A-8497791 0.071014145 0.006420784 1 1
SNP_A-1909444 0.433298117 0.487344503 1 1
SNP_A-8358063 -0.120802974 0.045802832 1 1
SNP_A-8329892 -0.308989189 0.002110105 1 1
SNP_A-8408912 -0.115377318 0.471444786 1 1
SNP_A-8294056 -0.107993203 0.558844268 1 1
SNP_A-1886933 -0.074763943 0.516260564 1 1
SNP_A-2236359 -0.198094884 1.045093298 1 1
SNP_A-8515688 0.345273388 0.470917732 1 1
SNP_A-2205441 0.291113951 -0.061362818 1 1
SNP_A-8524447 0.30825212 0.045043081 1 1
SNP_A-8573955 0.487829343 1.089814901 1 1
SNP_A-8530278 0.409285501 1.074035168 1 1
SNP_A-8573668 0.299636675 1.063412666 1 1
SNP_A-8573414 0.29222188 0.401596278 1 1
SNP_A-8531044 0.859449761 1.001776218 1 1

Total number of rows: 931633

Table truncated, full table size 38569 Kbytes.

Supplementary file Size Download File type/resource
GSM1815840_T065.CEL.gz 29.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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