{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE319nnn/GSE319926/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Homo sapiens"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE319926"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs","description":"Conventional RNA extraction with acid guanidinium thiocyanate–phenol–chloroform (AGPC) reagents incompletely recovers a subset of transcripts, termed semi-extractable RNAs (seRNAs). This underrepresented RNA population includes architectural RNAs (arcRNAs), which scaffold membraneless organelles, as well as stress-induced downstream-of-gene readthrough transcripts (DoGs). Although our previously developed “improved” AGPC protocol incorporating physical disruption enhances seRNA recovery, it also co-extracts abundant, readily extractable RNAs, yielding mixed populations that hinder precise characterization of seRNAs. Here, we present SERIPH (Semi-Extractable RNA Isolation from the InterPHase), a simple two-step protocol that selectively enriches seRNAs by separating them from readily extractable RNA species. By depleting abundant extractable RNAs, SERIPH increases detection sensitivity, enabling the capture of weakly semi-extractable transcripts, including those of low abundance, that were overlooked by previous approaches. This increased sensitivity expands the detectable seRNA repertoire and reveals a broader genomic extent of DoG transcription than previously appreciated. Together, SERIPH provides a robust framework for high-resolution analysis of seRNA populations, advancing studies of RNA processing, transcriptional regulation, and RNA-mediated nuclear organization in stress responses and disease","dates":{"publication":"2026/06/27"},"accession":"GSE319926","cross_references":{"GSM":["GSM9529444","GSM9529445","GSM9529446","GSM9529447","GSM9529436","GSM9529437","GSM9529448","GSM9529449","GSM9529438","GSM9529439","GSM9529450","GSM9529440","GSM9529451","GSM9529441","GSM9529442","GSM9529443"],"GPL":["34281"],"GSE":["319926"],"taxon":["Homo sapiens"],"PMID":["[42350076]"]}}