biostudies-arrayexpressLinnéa ÖgrenSaccharomyces cerevisiaehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15116Whole genome UV footprinting in yeast using deamination sequencing (Deam-seq), wherein photoproducts induced by high-dose UVB irradiation are revealed as mutations. In Deam-seq, cytosines within cyclobutane pyrimidine dimers (CPDs) are converted to uracil by rapid deamination at elevated temperature. Following CPD repair by photolyase, samples were sequenced at ultra-deep (>7,000×) coverage, enabling calculation of per-base damage fractions (mutant allele frequencies). By comparing cellular and naked DNA, this approach can pinpoint genomic sites bound by proteins that modulate UV damage.biostudies-arrayexpressSequencing - Paired-end Illumina high-throughput sequencing (NovaSeq 6000).Sample Collection - Cells were grown in YPD media at 30 degrees Celsius. Suspension cells exposed to UV light in petri dishes were pelleted by centrifugation.Library Construction - Deam-seq libraries built using UMI-containing Illumina adapters.Nucleic Acid Extraction - DNA isolation was performed using the YeaStar Genomic DNA kit (Zymo Research, D2002) and according to the manufacturer’s instructions.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads were mapped to the SacCer3 reference genome using BWA mem, sorted using samtools and deduplicated using umi-tools. Variants were called using VarScan (options mpileup2cns --min-coverage 0 --min-reads2 0 --strand-filter 0 --p- value 1.00 --min-var-freq 0) together with samtools pileup (options -B -q 10 -Q25 -d 1000000). Pairwise comparisons of damage allele frequencies between samples were made by computing log2 ratios. These were then normalized by pentanucleotide sequence contexts to obtain the final WIG-files.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000DNA-seqSaccharomyces cerevisiaeLinnéa ÖgrenfalseYeast Deam-seqWhole genome UV footprinting in yeast using deamination sequencing (Deam-seq), wherein photoproducts induced by high-dose UVB irradiation are revealed as mutations. In Deam-seq, cytosines within cyclobutane pyrimidine dimers (CPDs) are converted to uracil by rapid deamination at elevated temperature. Following CPD repair by photolyase, samples were sequenced at ultra-deep (>7,000×) coverage, enabling calculation of per-base damage fractions (mutant allele frequencies). By comparing cellular and naked DNA, this approach can pinpoint genomic sites bound by proteins that modulate UV damage.2025-04-28T00:00:00Z2026-01-05T12:23:49.468Z2025-05-02T15:56:41.641ZE-MTAB-15116ERP166146EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0003816EFO_0004184