{"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-17008"],"description":["Whole genome UV footprinting in yeast using deamination sequencing (Deam-seq), wherein photoproducts induced by high-dose UVC 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. The samples were irradiated with UVC on ice, for 45 seconds. Raw fastq files are available in ENA (accession: PRJEB111787)."],"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":["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":"Light-based footprinting of a eukaryotic genome","description":"Whole genome UV footprinting in yeast using deamination sequencing (Deam-seq), wherein photoproducts induced by high-dose UVC 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. The samples were irradiated with UVC on ice, for 45 seconds. Raw fastq files are available in ENA (accession: PRJEB111787).","dates":{"release":"2026-05-07T00:00:00Z","modification":"2026-05-07T13:55:02.143Z","creation":"2026-05-06T12:25:46.811Z"},"accession":"E-MTAB-17008","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}