{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE318nnn/GSE318343/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"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=GSE318343"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"PCRD-seq: Proximity Crosslinking-induced RNA Depletion for Low-Input Chromatin-associated Transcriptome Profiling","description":"Chromatin-associated RNAs play critical roles in regulating chromatin organization and transcription, underscoring the importance of their study. Proximity labeling has emerged as a promising and versatile technique for profiling chromatin-associated RNAs with high spatiotemporal resolution. While being a powerful technique, traditional proximity labeling methods depend on complex, high-input enrichment protocols, which significantly limit their wide practical application. Here, we developed a straightforward, enrichment-free chromatin-associated RNA profiling strategy: Proximity Crosslinking-induced RNA Depletion sequencing (PCRD-seq). This approach leverages the proximity crosslinking between chromatin and its surrounding RNAs induced by singlet oxygen generated by HoeDBF, a photosensitizer targeting chromatin region. The proximity crosslinking hinders the release of chromatin-associated RNAs during routine TRIzol extraction, consequently leading to a specific depletion of these RNAs. This method was successfully applied to investigate the role of U1 snRNA in RNA chromatin retention and the differences in chromatin-associated transcriptomes between two ovarian cancer cell lines with opposite metastatic capability. Moreover, our PCRD-seq exhibits potential in profiling nuclear lamina-associated RNAs, which paves the way for its application to profile RNAs associated with other chromatin subdomains. The minimal cell input and simple workflow endow PCRD-seq as a transformative tool for wide applications.","dates":{"publication":"2026/09/16"},"accession":"GSE318343","cross_references":{"GSM":["GSM9492821","GSM9492788","GSM9492789","GSM9492822","GSM9492786","GSM9492787","GSM9492820","GSM9492825","GSM9492826","GSM9492823","GSM9492824","GSM9492829","GSM9492827","GSM9492828","GSM9492791","GSM9492792","GSM9492790","GSM9492795","GSM9492796","GSM9492793","GSM9492794","GSM9492832","GSM9492799","GSM9492833","GSM9492830","GSM9492797","GSM9492831","GSM9492798","GSM9492836","GSM9492837","GSM9492834","GSM9492835","GSM9492838","GSM9492839","GSM9492840","GSM9492766","GSM9492843","GSM9492844","GSM9492767","GSM9492800","GSM9492841","GSM9492842","GSM9492847","GSM9492803","GSM9492804","GSM9492848","GSM9492801","GSM9492768","GSM9492845","GSM9492769","GSM9492846","GSM9492802","GSM9492807","GSM9492808","GSM9492849","GSM9492805","GSM9492806","GSM9492809","GSM9492770","GSM9492773","GSM9492850","GSM9492774","GSM9492851","GSM9492771","GSM9492772","GSM9492810","GSM9492777","GSM9492778","GSM9492811","GSM9492852","GSM9492775","GSM9492776","GSM9492814","GSM9492815","GSM9492812","GSM9492779","GSM9492813","GSM9492818","GSM9492819","GSM9492816","GSM9492817","GSM9492780","GSM9492781","GSM9492784","GSM9492785","GSM9492782","GSM9492783"],"GPL":["20795","24676","34284"],"GSE":["318343"],"taxon":["Homo sapiens"],"PMID":["[42644390]"]}}