{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE295nnn/GSE295080/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Mus musculus"," Escherichia coli"," Adeno-associated virus 9"," Homo sapiens"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE295080"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Disambiguating Transcriptional Effects from Post-Transcriptional Effects of Genetic Variants with an Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA).","description":"Some widely used methods to study functional effects of DNA sequence on transcription cannot readily disambiguate these from post-transcriptional impacts of the same element on RNA. Therefore, we developed an approach enabling assessment of DNA/RNA regulatory elements in parallel: Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA). ISOMPRA quantifies pre-spliced RNA to more directly assess transcription rate, and spliced RNA, corrected for transcription rate, to correctly identify RNA stability-altering 3’ UTR elements. We benchmark ISOMPRA with both predicted enhancers and 3’ UTR elements, selected regions containing autism patient mutations. We identify numerous functional enhancers/UTRs, and discover a subset with high impact mutations. We further show failing to consider both potential transcriptional and post transcriptional effects results in numerous false-positives and false-negatives. Finally, we adapt ISOMPRA for in vivo analysis of element effects via AAV transduction. Combined with Cre-dependent priming sites, this permits analyses of both transcriptional and post-transcriptional effects within specific cell types of the brain, and further enables measurement of regulatory impacts of in vivo traits, such as sex.","dates":{"publication":"2025/12/12"},"accession":"GSE295080","cross_references":{"GSM":["GSM8941903","GSM8941902","GSM8941905","GSM8941904","GSM8941901","GSM8941900","GSM9188122","GSM9188123","GSM9188124","GSM9188125","GSM9188126","GSM9188127","GSM9188128","GSM9188129","GSM9188120","GSM9188121","GSM9188119","GSM9188133","GSM9188134","GSM9188135","GSM9188136","GSM9188137","GSM9188138","GSM9188139","GSM9188130","GSM9188131","GSM9188132","GSM8941899","GSM8941898","GSM8941895","GSM8941894","GSM8941897","GSM8941896","GSM8941891","GSM8941890","GSM8941893","GSM8941892","GSM8942064","GSM8942062","GSM8942063","GSM8942060","GSM8942061","GSM8941877","GSM8941998","GSM8941876","GSM8941997","GSM8941879","GSM8941999","GSM8941878","GSM8941873","GSM8941994","GSM8941993","GSM8941872","GSM8941996","GSM8942048","GSM8941875","GSM8941874","GSM8942049","GSM8941995","GSM8941990","GSM8942046","GSM8942047","GSM8941871","GSM8941992","GSM8942044","GSM8941870","GSM8942045","GSM8941991","GSM8942042","GSM8942043","GSM8942040","GSM8942041","GSM8941888","GSM8941887","GSM8941889","GSM8941884","GSM8941883","GSM8942059","GSM8941886","GSM8941885","GSM8942057","GSM8941880","GSM8942058","GSM8941882","GSM8942055","GSM8941881","GSM8942056","GSM8942053","GSM8942054","GSM8942051","GSM8942052","GSM8942050","GSM8941859","GSM8941858","GSM8941979","GSM8941976","GSM8941855","GSM8941854","GSM8941975","GSM8941857","GSM8941978","GSM8941856","GSM8941977","GSM8942028","GSM8941851","GSM8941972","GSM8941850","GSM8941971","GSM8942029","GSM8941853","GSM8941974","GSM8942026","GSM8942027","GSM8941973","GSM8941852","GSM8942024","GSM8942025","GSM8941970","GSM8942022","GSM8942023","GSM8942020","GSM8942021","GSM8941869","GSM8941987","GSM8941866","GSM8941865","GSM8941986","GSM8941868","GSM8941989","GSM8941867","GSM8941988","GSM8942039","GSM8941862","GSM8941983","GSM8941861","GSM8941982","GSM8941864","GSM8941985","GSM8942037","GSM8941984","GSM8941863","GSM8942038","GSM8942035","GSM8942036","GSM8942033","GSM8941860","GSM8941981","GSM8942034","GSM8941980","GSM8942031","GSM8942032","GSM8942030","GSM8941837","GSM8941958","GSM8941836","GSM8941957","GSM8941839","GSM8941838","GSM8941959","GSM8941833","GSM8941954","GSM8941953","GSM8941832","GSM8941956","GSM8942008","GSM8941835","GSM8941834","GSM8942009","GSM8941955","GSM8941950","GSM8942006","GSM8942007","GSM8942004","GSM8941831","GSM8941952","GSM8941830","GSM8942005","GSM8941951","GSM8942002","GSM8942003","GSM8942000","GSM8942001","GSM8941829","GSM8941848","GSM8941969","GSM8941847","GSM8941968","GSM8941849","GSM8941844","GSM8941965","GSM8941964","GSM8941843","GSM8941967","GSM8942019","GSM8941846","GSM8941845","GSM8941966","GSM8942017","GSM8941840","GSM8941961","GSM8941960","GSM8942018","GSM8941842","GSM8941963","GSM8942015","GSM8941841","GSM8942016","GSM8941962","GSM8942013","GSM8942014","GSM8942011","GSM9188099","GSM8942012","GSM8942010","GSM8941936","GSM9188100","GSM8941815","GSM9188101","GSM8941814","GSM8941935","GSM9188102","GSM8941817","GSM8941938","GSM8941816","GSM8941937","GSM9188103","GSM9188104","GSM8941811","GSM8941932","GSM8941810","GSM8941931","GSM9188105","GSM8941813","GSM8941934","GSM9188106","GSM8941933","GSM9188107","GSM8941812","GSM8941930","GSM8941929","GSM8941928","GSM8941809","GSM8941947","GSM9188111","GSM8941826","GSM9188112","GSM8941825","GSM8941946","GSM9188113","GSM8941828","GSM8941949","GSM8941827","GSM8941948","GSM9188114","GSM9188115","GSM8941822","GSM8941943","GSM8941821","GSM8941942","GSM9188116","GSM8941824","GSM8941945","GSM9188117","GSM8941944","GSM9188118","GSM8941823","GSM8941941","GSM8941820","GSM8941940","GSM9188110","GSM9188108","GSM9188109","GSM8941819","GSM8941818","GSM8941939","GSM8941914","GSM8941913","GSM8941916","GSM8941915","GSM8941910","GSM8941912","GSM8941911","GSM8941907","GSM8941906","GSM8941909","GSM8941908","GSM8941925","GSM8941924","GSM8941927","GSM8941926","GSM8941921","GSM8941920","GSM8941923","GSM8941922","GSM8941918","GSM8941917","GSM8941919"],"GPL":["35777","35101","34281","34328"],"GSE":["295080"],"taxon":["Mus musculus"," Escherichia coli"," Adeno-associated virus 9"," Homo sapiens"]}}