{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE281nnn/GSE281920/"]},"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=GSE281920"],"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 [scRepli-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":"GSE281920","cross_references":{"GSM":["GSM8632681","GSM8632560","GSM8632680","GSM8632683","GSM8632562","GSM8632561","GSM8632682","GSM8632564","GSM8632685","GSM8632684","GSM8632563","GSM8632687","GSM8632566","GSM8632686","GSM8632565","GSM8632689","GSM8632568","GSM8632567","GSM8632688","GSM8632569","GSM8632670","GSM8632791","GSM8632790","GSM8632793","GSM8632672","GSM8632551","GSM8632792","GSM8632671","GSM8632550","GSM8632795","GSM8632674","GSM8632553","GSM8632673","GSM8632552","GSM8632794","GSM8632555","GSM8632797","GSM8632676","GSM8632796","GSM8632675","GSM8632554","GSM8632799","GSM8632678","GSM8632557","GSM8632798","GSM8632677","GSM8632556","GSM8632559","GSM8632558","GSM8632679","GSM8632582","GSM8632581","GSM8632584","GSM8632583","GSM8632586","GSM8632585","GSM8632588","GSM8632587","GSM8632589","GSM8632580","GSM8632692","GSM8632571","GSM8632570","GSM8632691","GSM8632694","GSM8632573","GSM8632693","GSM8632572","GSM8632575","GSM8632696","GSM8632695","GSM8632574","GSM8632698","GSM8632577","GSM8632697","GSM8632576","GSM8632579","GSM8632578","GSM8632699","GSM8632690","GSM8632760","GSM8632641","GSM8632520","GSM8632762","GSM8632761","GSM8632640","GSM8632764","GSM8632643","GSM8632522","GSM8632521","GSM8632763","GSM8632642","GSM8632524","GSM8632766","GSM8632645","GSM8632644","GSM8632523","GSM8632765","GSM8632647","GSM8632526","GSM8632768","GSM8632767","GSM8632646","GSM8632525","GSM8632649","GSM8632528","GSM8632527","GSM8632769","GSM8632648","GSM8632529","GSM8632630","GSM8632751","GSM8632750","GSM8632753","GSM8632632","GSM8632752","GSM8632631","GSM8632755","GSM8632634","GSM8632754","GSM8632633","GSM8632515","GSM8632757","GSM8632636","GSM8632756","GSM8632635","GSM8632638","GSM8632517","GSM8632759","GSM8632758","GSM8632637","GSM8632516","GSM8632519","GSM8632518","GSM8632639","GSM8632780","GSM8632661","GSM8632540","GSM8632782","GSM8632781","GSM8632660","GSM8632784","GSM8632663","GSM8632542","GSM8632541","GSM8632783","GSM8632662","GSM8632544","GSM8632786","GSM8632665","GSM8632664","GSM8632543","GSM8632785","GSM8632667","GSM8632546","GSM8632788","GSM8632787","GSM8632666","GSM8632545","GSM8632669","GSM8632548","GSM8632547","GSM8632789","GSM8632668","GSM8632549","GSM8632650","GSM8632771","GSM8632770","GSM8632773","GSM8632652","GSM8632531","GSM8632772","GSM8632651","GSM8632530","GSM8632775","GSM8632654","GSM8632533","GSM8632653","GSM8632532","GSM8632774","GSM8632535","GSM8632777","GSM8632656","GSM8632776","GSM8632655","GSM8632534","GSM8632658","GSM8632537","GSM8632779","GSM8632778","GSM8632657","GSM8632536","GSM8632539","GSM8632538","GSM8632659","GSM8632841","GSM8632720","GSM8632840","GSM8632601","GSM8632843","GSM8632722","GSM8632721","GSM8632600","GSM8632842","GSM8632724","GSM8632603","GSM8632845","GSM8632844","GSM8632723","GSM8632602","GSM8632847","GSM8632726","GSM8632605","GSM8632604","GSM8632846","GSM8632725","GSM8632607","GSM8632849","GSM8632728","GSM8632727","GSM8632606","GSM8632848","GSM8632719","GSM8632839","GSM8632718","GSM8632830","GSM8632832","GSM8632711","GSM8632710","GSM8632831","GSM8632713","GSM8632834","GSM8632833","GSM8632712","GSM8632836","GSM8632715","GSM8632835","GSM8632714","GSM8632838","GSM8632717","GSM8632837","GSM8632716","GSM8632829","GSM8632708","GSM8632707","GSM8632828","GSM8632709","GSM8632740","GSM8632621","GSM8632742","GSM8632741","GSM8632620","GSM8632744","GSM8632623","GSM8632743","GSM8632622","GSM8632746","GSM8632625","GSM8632624","GSM8632745","GSM8632627","GSM8632748","GSM8632747","GSM8632626","GSM8632629","GSM8632749","GSM8632628","GSM8632619","GSM8632610","GSM8632731","GSM8632730","GSM8632733","GSM8632612","GSM8632732","GSM8632611","GSM8632735","GSM8632614","GSM8632734","GSM8632613","GSM8632737","GSM8632616","GSM8632736","GSM8632615","GSM8632618","GSM8632739","GSM8632738","GSM8632617","GSM8632609","GSM8632729","GSM8632608","GSM8632801","GSM8632800","GSM8632803","GSM8632802","GSM8632805","GSM8632804","GSM8632593","GSM8632592","GSM8632595","GSM8632594","GSM8632597","GSM8632596","GSM8632599","GSM8632598","GSM8632591","GSM8632590","GSM8632821","GSM8632700","GSM8632820","GSM8632823","GSM8632702","GSM8632701","GSM8632822","GSM8632704","GSM8632825","GSM8632824","GSM8632703","GSM8632827","GSM8632706","GSM8632826","GSM8632705","GSM8632818","GSM8632817","GSM8632819","GSM8632810","GSM8632812","GSM8632811","GSM8632814","GSM8632813","GSM8632816","GSM8632815","GSM8632807","GSM8632806","GSM8632809","GSM8632808"],"GPL":["20795","21273"],"GSE":["281920"],"taxon":[" Mus musculus","Homo sapiens"]}}