ABSTRACT: CASE SAMPLES USING Affymetrix SNP6.0 technology (Thermo Fisher Scientific company): OncoScan FFPE Assay Kit was used for FFPE tissue samples (designed for degraded DNA) and the Cytoscan HD Array Kit was used for the fresh-frozen tissues
Project description:Genome-Wide Human SNP Array 6.0 or the CytoScan HD array, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) now part of Thermo Fisher Scientific (Thermo Fisher Scientific, Inc.)
Project description:Hybridization-based genomic profiling arrays were performed using Genome-Wide Human SNP Array 6.0 or the CytoScan HD array, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) now part of Thermo Fisher Scientific (Thermo Fisher Scientific, Inc.) Following the procedures of sample preparation, hybridization, and scanning, the CEL file of Genome-Wide
Human SNP Array 6.0 was analyzed as previously described (Magrangeas et al. 2012) and the CEL file of CytoScan HD array was analyzed using the Chromosome Analysis Suite (ChAS) software (Thermo Fisher Scientific, Inc).
Project description:we used single-cell transcriptomics and genotyping arrays to characterize 17 neuroblastoma samples across different risk groups and genetic subsets.Fresh samples, obtained from surgical resections and core biopsies, were used for genome variation profiling. DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent). SNP microarray analysis was performed using the Cytoscan HD Array (Affymetrix) and data was processed using the Chromosome Analysis Suite version 3.3.0.139.
