{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE299nnn/GSE299609/"]},"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=GSE299609"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Hydrogel Microencapsulation Enables High-Sensitivity Mitochondrial RNA Profiling from Ultra-Low Input Samples","description":"The 13 protein-coding genes encoded by the mitochondrial genome are essential markers for cellular energy metabolism and diverse physiological and pathological processes. However, conventional RNA-seq methods often suffer from poor sensitivity in detecting mitochondrial transcripts due to their low abundance, vulnerability to degradation, and loss during sample preparation. Here, we present a hydrogel-assisted RNA sequencing strategy that encapsulates individual RNA molecules within semi-permeable core-shell microgels (~80 μm in diameter), enabling ultra-low-input profiling, approximately equivalent to one RNA molecule per each of 1.2 million nanoliter-scale compartments. This spatial confinement minimizes intermolecular interactions, preserves mitochondrial RNA integrity, and enhances both reverse transcription and Tn5 tagmentation efficiency of mitochondrial RNA molecules. Compared with conventional RNA-seq, our method significantly improves the detection of all 13 protein-coding mitochondrial genes, even with minimal RNA input (~1 ng) and low sequencing depth (~1 million reads). This strategy provides a robust, cost-effective, and scalable approach for accurate and reproducible profiling of mitochondrial transcripts, establishing a powerful tool for investigating mitochondrial function in low-input or precious samples, with broad implications for biomedical research and clinical diagnostics.","dates":{"publication":"2026/09/01"},"accession":"GSE299609","cross_references":{"GSM":["GSM9042000","GSM9042001","GSM9042002","GSM9042003","GSM9042004","GSM9041996","GSM9041997","GSM9041998","GSM9041999"],"GPL":["24676"],"GSE":["299609"],"taxon":["Homo sapiens"]}}