GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE299nnn/GSE299609/primary200OKTranscriptomicsHomo sapiensExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299609GEOGSEfalseHydrogel Microencapsulation Enables High-Sensitivity Mitochondrial RNA Profiling from Ultra-Low Input SamplesThe 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.2026/09/01GSE299609GSM9042000GSM9042001GSM9042002GSM9042003GSM9042004GSM9041996GSM9041997GSM9041998GSM904199924676299609Homo sapiens