Comprehensive single-nucleus molecular and cell profiling features for cardiac tissues across platforms

ABSTRACT: Single-nucleus RNA sequencing (snRNA-Seq) enables high-resolution transcriptomic profiling of complex tissues such as the heart, where dissociation into intact single cells is challenging. Among the commercially available snRNA-Seq platforms, 10X Genomics Chromium and Takara Bio’s ICELL8 cx represent technically distinct approaches. However, a systematic comparison of their performance in cardiac tissue remains limited. Here, we benchmarked the 3’-Chromium, 5’-Chromium, and ICELL8 cx platforms using nuclei isolated from both mouse and human heart tissues, including healthy donor samples and those from patients with non-ischemic cardiomyopathy. We evaluated key metrics including nuclei capture efficiency, library complexity, transcript detection sensitivity, RNA biotype coverage, ambient RNA contamination, and cell type resolution. Our results show that the Chromium platforms yield higher nuclear throughput with robust capture efficiency and low contamination, whereas ICELL8 cx provides deeper transcriptomic coverage per nucleus, detecting a broader diversity of RNA biotypes, including low-abundance non-coding RNAs, albeit with lower total nuclei captured. Both platforms resolved major cardiac cell populations with consistent cell-type proportions and marker gene expression. These findings provide a practical guide for selecting snRNA-Seq workflows optimized for cardiac tissue research, balancing trade-offs between cell throughput and transcriptome depth.

ORGANISM(S): Mus musculus

PROVIDER: GSE316945 | GEO | 2026/08/11

REPOSITORIES: GEO