{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE143nnn/GSE143917/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Mus musculus"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143917"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"DNA-RNA three-stranded hybrids: from the telomere to the genome (mouse dataset)","description":"The origin and possible functions of local three-stranded DNA-RNA hybrid regions in the mammalian genome is still a matter of discussion. R-loops have been so far essentially detected by immunodetection of the DNA-RNA hybrid regions (DRIP assay). This powerful and easy to implement method relies on recognition by a unique monoclonal antibody and may not detect all the hybrid regions. Starting from simple logical steps, we developed a preparative method that allows detection and physical isolation of stable DNA-RNA triplexes in a complex genome. A modification of the popular TRIzol extraction procedure first identifies RNAs stably bound to DNA in RNaseH-sensitive complexes, which can be isolated and further characterized by RNA-seq. We first tested the efficiency of the approach by a search for a generalized three-stranded state of the human and mouse telomeres. While such a structure is suggested by the complementarity of the long chromosomal CCCTAA repeats and the noncoding RNA TERRA, it was only in one class of cancer cells that telomeric R-loops were so far evidenced by DRIP assay. The proposed method allowed us to generalize to the mouse and human genomes the notion of terminal R-loop complexes with TERRA molecules synthesized from local promoters. When further applied to murine sperm genome, it evidenced a reproducible genome-wide profile of RNA complexes.","dates":{"publication":"2021/06/30"},"accession":"GSE143917","cross_references":{"GSM":["GSM4276629","GSM4276628","GSM4276627","GSM4276638","GSM4276637","GSM4276636","GSM4276635","GSM4276634","GSM4276633","GSM4276632","GSM4276631","GSM4276630"],"GPL":["17021"],"SRA":["SRP243001"],"GSE":["143917"],"taxon":["Mus musculus"]}}