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Series GSE37977 Query DataSets for GSE37977
Status Public on Nov 26, 2012
Title SNP6.0 copy number analysis of eight diffuse large B-cell samples and one matched blood sample
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the SNP6.0 data. GEO submission, GSE37978 contains the Cyto2.7M data.
Overall design DNA was extracted from eight samples of diffuse-large B-cell lymphoma with complex genomic rearrangements using the DNeasy Blood & Tissue kit (Qiagen) following manufactures instructions. DNA was also included from one matched blood sample where mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific).
Copy number analysis of Affymetrix SNP6.0 arrays was performed on eight diffuse large B-cell samples and one matched blood sample.
Contributor(s) Bødker JS, Gyrup C, Johansen P, Schmitz A, Madsen J, Johnsen HE, Boegsted M, Dybkær K, Nyegaard M
Citation(s) 23182917
Submission date May 14, 2012
Last update date Nov 27, 2018
Contact name Julie Støve Bødker
Organization name Aalborg University Hospital
Department Department of Heamatology
Lab Research Laboratory
Street address Sdr. Skovvej 15
City Aalborg
ZIP/Postal code 9000
Country Denmark
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (9)
GSM931247 BB39
GSM931248 H35
GSM931249 H285
This SubSeries is part of SuperSeries:
GSE37979 Performance Comparison of the Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-genome Microarrays in Complex Cancer Samples
BioProject PRJNA167158

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37977_RAW.tar 575.9 Mb (http)(custom) TAR (of CEL, CNCHP)
GSE37977_summarized_results.txt.gz 189.9 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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