array comparative genomic hybridization (acgh) platform 60,000 oligonucleotides  (Agilent technologies)

Journal: Genes & Development

Article Title: Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability

doi: 10.1101/gad.350618.123

Figure Lengend Snippet: MIR frequently causes additional unselected rearrangements. ( A ) Experimental system in diploid S. cerevisiae . The heterozygous DSB-inducible YS -HOcs construct replaces URA3 on chromosome V. The LY and S2 donors consist in the two halves of the LYS2 gene (2090 and 2089 bp, respectively) at its locus on chromosome II. This DSB donor configuration is referred to as interchromosomal with allelic donors. Translocation of the LY and S2 donors restores a functional LYS2 gene. Approximately 10% of induced Lys + colonies are small on the initial plate and exhibit a higher proportion of additional SVs than bigger colonies. ( B – D ) Twelve small MIR recombinants were analyzed by Southern blot ( B ), PFGE ( C ), and high-throughput shotgun sequencing ( D ). Strains labeled in green were additionally analyzed by aCGH and nanopore long-read sequencing. ( C ) The ladder corresponds to a S. cerevisiae strain from the YPH80 background, marginally different from our W303 parental strain. Ladder size is in kilobases. Chromosome V and chromosome VIII comigrate in the W303 background. (*) Chromosomal abnormality. ( E ) Deduced genome structure of the 12 MIR recombinants. The number of nanopore (NP) reads encompassing the unselected rearrangements is indicated.

Article Snippet: Array comparative genomic hybridization (aCGH) copy number profiling and characterization of rearrangement junctions through Oxford nanopore long-read sequencing were carried out following procedures described previously ( ; ).

Techniques: Construct, Translocation Assay, Functional Assay, Southern Blot, High Throughput Screening Assay, Shotgun Sequencing, Labeling, Sequencing