Genome-wide SNP Analysis of Cell Lines

We performed genome wide single nucleotide polymorphism (SNP) analysis using SNP 6.0 arrays (Affymetrix, High Wycombe, U.K) on SKM1-S and SKM1-R cell lines. DNA was prepared for hybridization according to the manufacturers' recommendations. Affymetrix CEL files for each sample were analyzed using the Genotyping Console software (v3.0.2). Genotyping was performed using Birdseed V2 algorithm. Unpaired Copy Number and LOH analysis was performed with Regional GC correction. Copy number and UPD were also analyzed using the Copy Number Analyzer for GeneChip (CNAG version 3.3.0.1) algorithm (http://www.genome.umin.jp/CNAGtop2.html) [28 (link)].

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Cluzeau T., Dubois A., Jacquel A., Luciano F., Renneville A., Preudhomme C., Karsenti J.M., Mounier N., Rohrlich P., Raynaud S., Mari B., Robert G, & Auberger P. (2014). Phenotypic and genotypic characterization of azacitidine-sensitive and resistant SKM1 myeloid cell lines. Oncotarget, 5(12), 4384-4391.

Publication 2014

SNP 6.0 arrays Genotyping Console software

Cell lines Genechip Genome Hybridization Single nucleotide polymorphism

Corresponding Organization :

Other organizations : Inserm, Université Côte d'Azur, La Ligue Contre le Cancer, Centre Hospitalier Universitaire de Nice, Centre Méditerranéen de Médecine Moléculaire, Lille’s Cardiology Hospital, Centre National de la Recherche Scientifique

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Variable analysis

independent variables

Genome wide single nucleotide polymorphism (SNP) analysis using SNP 6.0 arrays (Affymetrix, High Wycombe, U.K)

dependent variables

Copy number and UPD
Genotyping

control variables

DNA was prepared for hybridization according to the manufacturers' recommendations
Affymetrix CEL files for each sample were analyzed using the Genotyping Console software (v3.0.2)
Genotyping was performed using Birdseed V2 algorithm
Unpaired Copy Number and LOH analysis was performed with Regional GC correction
Copy number and UPD were also analyzed using the Copy Number Analyzer for GeneChip (CNAG version 3.3.0.1) algorithm

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