{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Linnéa Ögren"],"organism":["Saccharomyces cerevisiae"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15116"],"description":["Whole 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["DNA-seq"],"species":["Saccharomyces cerevisiae"],"pubmed_authors":["Linnéa Ögren"],"additional_accession":[]},"is_claimable":false,"name":"Yeast Deam-seq","description":"Whole 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.","dates":{"release":"2025-04-28T00:00:00Z","modification":"2026-01-05T12:23:49.468Z","creation":"2025-05-02T15:56:41.641Z"},"accession":"E-MTAB-15116","cross_references":{"ENA":["ERP166146"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}