{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lei Qi"],"organism":["Saccharomyces cerevisiae"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16051"],"description":["This study investigates a mitotic recombination hotspot on the right arm of chromosome VII in Saccharomyces cerevisiae. Using Agilent two-color comparative genomic hybridization arrays, we compared genome-wide and chromosome-specific LOH patterns between pol32Δ and isogenic wild-type diploids. The data reveal distinct recombination signatures at the VII-R hotspot in wild type strains, including elevated crossover frequency and complex LOH tracts indicative of aberrant repair of replication-associated breaks."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Genomic DNA was extracted from yeast colonies embedded in low-melting-point agarose plugs to preserve chromosomal integrity. Cells were lysed with zymolyase and proteinase K, and plugs were extensively washed. DNA was recovered from the plugs by phenol–chloroform extraction and ethanol precipitation, followed by gentle sonication to generate fragments of approximately 400 bp. DNA quality and concentration were confirmed by agarose gel electrophoresis and spectrophotometry prior to labeling.","Labeling - DNA from individual 5-FOAʳ His⁺ colonies was labeled with Cy5-dUTP, while genomic DNA from control (JSC25) colonies was labeled with Cy3-dUTP, using the BioPrime DNA Labeling System (Invitrogen). Labeled DNAs were purified using QIAquick columns (Qiagen) and quantified spectrophotometrically.","Growth Protocol - Yeast cultures were grown in YPD medium at 30 °C for 5-FOA selection. No external treatment or chemical exposure was applied. Colonies were only selected based on resistance to 5-fluoroorotic acid (5-FOA) and confirmed for growth on SD-His⁻ plates.","Sample Collection - Diploid yeast strains (QL90, wild type; QL92, pol32Δ) carrying heterozygous HIS3 and URA3 insertions on the right arm of chromosome VII were grown on YPD medium at 30 °C. Mitotic recombination derivatives were selected on medium containing 5-fluoroorotic acid (5-FOA). Colonies with the 5-FOAʳ His⁺ phenotype were isolated for further genomic analysis.","Hybridization - Equal amounts of Cy3- and Cy5-labeled DNA samples were mixed and hybridized competitively to custom yeast SNP microarrays at 62 °C for 16 h in a hybridization oven, following the procedure of St. Charles et al. (2012). Post-hybridization washes were performed with Agilent wash buffers 1 and 2 under standard conditions.","Scaning - Arrays were scanned using an Agilent Microarray Scanner at 5 μm resolution, and raw signal intensities were extracted with Agilent Feature Extraction Software (v12.0). The Cy5/Cy3 hybridization ratios were calculated and analyzed as previously described (St. Charles et.al. 2012) to determine LOH and crossover breakpoints.","Sample Treatment - Recombinant colonies were selected based on resistance to 5-fluoroorotic acid (5-FOA) and confirmed for histidine prototrophy on SD-His⁻ medium."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Microarray intensity data were normalized by the LOWESS method using Agilent Feature Extraction software prior to LOH mapping and visualization."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"study_type":["comparative genomic hybridization by array"],"species":["Saccharomyces cerevisiae"],"pubmed_title":["The multifaceted roles of the DNA polymerase subunit Pol32 in maintaining genome integrity"],"pubmed_authors":["Lei Qi"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide analysis of loss-of-heterozygosity and chromosomal rearrangements in Saccharomyces cerevisiae pol32Δ diploids using Agilent two-color microarrays","description":"This study investigates a mitotic recombination hotspot on the right arm of chromosome VII in Saccharomyces cerevisiae. Using Agilent two-color comparative genomic hybridization arrays, we compared genome-wide and chromosome-specific LOH patterns between pol32Δ and isogenic wild-type diploids. The data reveal distinct recombination signatures at the VII-R hotspot in wild type strains, including elevated crossover frequency and complex LOH tracts indicative of aberrant repair of replication-associated breaks.","dates":{"release":"2025-11-14T00:00:00Z","modification":"2026-05-27T14:36:26.453Z","creation":"2025-11-13T15:18:38.305Z"},"accession":"E-MTAB-16051","cross_references":{"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0000749","EFO_0005518","EFO_0003816","EFO_0003815","EFO_0003969"]}}