snPATHO-seq，一种多功能 FFPE 单细胞 RNA 测序方法，可解锁病理学档案。
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.
机构信息
Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
出版信息
Commun Biol. 2024 Oct 16;7(1):1340. doi: 10.1038/s42003-024-07043-2.
Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.
福尔马林固定石蜡包埋（FFPE）样本在单细胞组学研究中具有重要价值，但由于其 RNA 质量较低，尚未得到充分利用。在这项研究中，我们利用单细胞基因组技术的最新进展，引入了 snPATHO-seq，这是一种从 FFPE 样本中获取高质量单细胞转录组数据的通用方法。我们对 snPATHO-seq 工作流程的性能进行了基准测试，该工作流程与专门针对冷冻或新鲜样本的现有 10x 3' 和 Flex 测定法进行了比较，并突出了所有工作流程产生的 snRNA-seq 数据的一致性。snPATHO-seq 工作流程在经过广泛的健康和患病 FFPE 组织样本测试时也表现出了很高的稳健性。当与 FFPE 空间转录组学技术（如 FFPE Visium）结合使用时，snPATHO-seq 为 FFPE 样本提供了一种多模式采样方法，从而能够更全面地进行转录组特征分析。
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