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Sample GSM1586430 Query DataSets for GSM1586430
Status Public on Dec 23, 2017
Title Tumor, Splenic Diffuse Red Pulp Lymphoma, case 1_SPLEEN
Sample type genomic
 
Source name Spleen
Organism Homo sapiens
Characteristics tissue: spleen
cell type: splenic diffuse red pulp lymphoma
gender: female
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from peripheral blood or spleen samples using the Qiagen DNA Blood Mini/Midi Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
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 SNP 6.0
GSM1586429 and GSM1586430 are from the same patient and have the same CNCHP files.
Data processing Image data were analysed with Genotyping Console 4.0 to obtain the CEL data files, which were also exported to the Nexus Biodiscovery Edition for data analysis and visualization. Quality controls assessed by Genotyping Console included Contrast Quality Control (CQC>0.4) produced by Birdseed and Median of the Absolute values of all Pairwise Differences (MAPD<0.35). Tumour and normal DNA samples were analysed individually with the Nexus Biodiscovery Edition using the SNP-FASST2 segmentation algorithm and using segment reporting tool filters: minimum of 100 Kb minimum genomic size of a segment, as well as by visual inspection.
 
Submission date Jan 16, 2015
Last update date Dec 23, 2017
Contact name Alba Navarro
E-mail(s) ANAVARRL@clinic.ub.es
Organization name IDIBAPS - Hospital ClĂ­nic
Department Pathology
Lab Molecular Pathology
Street address Villaroel, 170
City Barcelona
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL6801
Series (2)
GSE64822 Clinical and molecular characterization of splenic diffuse red pulp lymphomas
GSE65052 Affymetrix SNP-array data for splenic diffuse red pulp lymphoma samples

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 1.000000 1 61723 -0.366310 0.984922 nan nan
CN_473964 1.000000 1 61796 -0.335128 0.984807 nan nan
CN_473965 1.000000 1 61811 -0.432644 0.984784 nan nan
CN_473981 1.000000 1 62908 -0.060222 0.983065 nan nan
CN_473982 1.000000 1 62925 -0.205698 0.983038 nan nan
CN_497981 1.000000 1 72764 -0.442159 0.967852 nan nan
CN_502615 1.000000 1 85924 -0.811954 0.948290 nan nan
CN_502613 1.000000 1 85986 -1.130978 0.948200 nan nan
CN_502614 1.000000 1 86312 -1.193947 0.947728 nan nan
CN_502616 1.000000 1 86329 -1.088680 0.947703 nan nan
CN_502843 1.000000 1 98590 -0.287356 0.930439 nan nan
CN_466171 2.000000 1 228694 0.039648 2.026103 nan nan
CN_468414 2.000000 1 229063 -0.310067 2.026013 nan nan
CN_468412 2.000000 1 229146 -0.313247 2.025993 nan nan
CN_468413 2.000000 1 229161 0.295172 2.025990 nan nan
CN_470565 2.000000 1 229607 0.642721 2.025881 nan nan
CN_468424 2.000000 1 235658 -0.310389 2.024408 nan nan
CN_468425 2.000000 1 235716 0.025561 2.024394 nan nan
CN_460512 2.000000 1 356431 0.017388 1.922877 nan nan
CN_460513 2.000000 1 356530 -0.079990 1.922877 nan nan

Total number of rows: 1813281

Table truncated, full table size 114241 Kbytes.




Supplementary file Size Download File type/resource
GSM1586430_Case_1_SPLEEN.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM1586430_Case_1_SPLEEN.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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