High-Throughput Single-Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer.

ABSTRACT: Puncture biopsy, especially those preserved by formalin fixed paraffin embedding (FFPE) samples, play an important role in various research purposes. Diverse single-nucleus RNA sequencing (snRNA-seq) techniques have been developed for FFPE samples, however, how to perform high-throughput snRNA-seq on small FFPE puncture samples is still a challenge. Here, the previously developed snRNA-seq technique (snRandom-seq) is optimized by implementing a pre-indexing procedure for the minimal puncture FFPE samples. In analyzing 20 samples from various solid tumors, optimized snRandom-seq still detected ≈17 000 genes and 12 000 long non-coding RNAs (lncRNAs), achieving precise clustering based on tissue origin. A head-to-head comparison with 10× Genomics on fresh biopsy samples showed a similar gene

SUBMITTER: Jiang W 

PROVIDER: S-EPMC11789576 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature