GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE318nnn/GSE318343/primaryOK200TranscriptomicsHomo sapiensExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE318343GEOGSEfalsePCRD-seq: Proximity Crosslinking-induced RNA Depletion for Low-Input Chromatin-associated Transcriptome ProfilingChromatin-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.2026/09/16GSE318343GSM9492821GSM9492788GSM9492789GSM9492822GSM9492786GSM9492787GSM9492820GSM9492825GSM9492826GSM9492823GSM9492824GSM9492829GSM9492827GSM9492828GSM9492791GSM9492792GSM9492790GSM9492795GSM9492796GSM9492793GSM9492794GSM9492832GSM9492799GSM9492833GSM9492830GSM9492797GSM9492831GSM9492798GSM9492836GSM9492837GSM9492834GSM9492835GSM9492838GSM9492839GSM9492840GSM9492766GSM9492843GSM9492844GSM9492767GSM9492800GSM9492841GSM9492842GSM9492847GSM9492803GSM9492804GSM9492848GSM9492801GSM9492768GSM9492845GSM9492769GSM9492846GSM9492802GSM9492807GSM9492808GSM9492849GSM9492805GSM9492806GSM9492809GSM9492770GSM9492773GSM9492850GSM9492774GSM9492851GSM9492771GSM9492772GSM9492810GSM9492777GSM9492778GSM9492811GSM9492852GSM9492775GSM9492776GSM9492814GSM9492815GSM9492812GSM9492779GSM9492813GSM9492818GSM9492819GSM9492816GSM9492817GSM9492780GSM9492781GSM9492784GSM9492785GSM9492782GSM9492783207952467634284318343Homo sapiens[42644390]