{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE281nnn/GSE281921/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Mus musculus"," Homo sapiens"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281921"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes [BrdU-IP Repli-seq]","description":"Common fragile sites (CFSs) are genomic regions susceptible to chromosome breaks. However, because they were identified using cell populations, low-frequency fragile sites (non-CFSs) could have been overlooked. Here we perform single-cell genome-wide mapping and classification of aphidicolin-induced chromosome breaks. In human osteosarcoma cells, 42% of breaks exhibit features of CFSs. The remaining 58% are non-CFSs that are ‘rare’ and replicate throughout the S-phase. Among non-CFSs, we identify early-S replicating breaks associated with transcription-replication conflicts, as well as two additional break classes. One is dependent on transcription and coincides with early-to-late-S replication timing (RT) transition regions, while another class exhibits late-S RT with its frequency increasing upon transcription inhibition. Intriguingly, we find that distinct RT landscapes are associated with aphidicolin-induced RT behavior and break classes. Our data reveal the frequencies, RT landscapes, and mechanistic differences among distinct break classes, providing a comprehensive view of genomic regions prone to breakage under replication stress.","dates":{"publication":"2026/07/13"},"accession":"GSE281921","cross_references":{"GSM":["GSM9344436","GSM8632850","GSM9344437","GSM8632852","GSM8632851","GSM8632854","GSM8632853","GSM8632856","GSM8632855","GSM8632858","GSM8632857","GSM8632859"],"GPL":["20795","21273"],"GSE":["281921"],"taxon":["Mus musculus"," Homo sapiens"]}}