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Sample GSM1815835 Query DataSets for GSM1815835
Status Public on Mar 03, 2016
Title N013
Sample type genomic
Source name Type II Enteropathy-associated T-cell lymphoma Sample N013
Organism Homo sapiens
Characteristics tissue type: Matched whole blood
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 4115.1489 0.0497 NA NA
SNP_A-8575115 8172.8281 0.9752 NA NA
SNP_A-8575371 7199.9463 0.875 NA NA
SNP_A-8709646 1144.4877 0.1732 NA NA
SNP_A-8497791 3107.1143 0.092 NA NA
SNP_A-1909444 5470.0381 0.4854 NA NA
SNP_A-8358063 4797.604 0.2765 NA NA
SNP_A-8329892 2493.645 0.0687 NA NA
SNP_A-8408912 3749.0405 0.4282 NA NA
SNP_A-8294056 1723.6495 0.5491 NA NA
SNP_A-1886933 2627.5007 0.4114 NA NA
SNP_A-2236359 4645.4248 0.8739 NA NA
SNP_A-8515688 4396.8096 0.4507 NA NA
SNP_A-2205441 5447.3647 0.1897 NA NA
SNP_A-8524447 4301.7773 0.3188 NA NA
SNP_A-8573955 1413.6843 0.3615 NA NA
SNP_A-8530278 2475.8438 0.7523 NA NA
SNP_A-8573668 1555.7058 0.7632 NA NA
SNP_A-8573414 1887.624 0.4842 NA NA
SNP_A-8531044 2413.1504 0.6221 NA NA

Total number of rows: 931633

Table truncated, full table size 33453 Kbytes.

Supplementary file Size Download File type/resource
GSM1815835_N013.CEL.gz 29.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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