Nature Communications (May 2023)

High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq

  • Ziye Xu,
  • Tianyu Zhang,
  • Hongyu Chen,
  • Yuyi Zhu,
  • Yuexiao Lv,
  • Shunji Zhang,
  • Jiaye Chen,
  • Haide Chen,
  • Lili Yang,
  • Weiqin Jiang,
  • Shengyu Ni,
  • Fangru Lu,
  • Zhaolun Wang,
  • Hao Yang,
  • Ling Dong,
  • Feng Chen,
  • Hong Zhang,
  • Yu Chen,
  • Jiong Liu,
  • Dandan Zhang,
  • Longjiang Fan,
  • Guoji Guo,
  • Yongcheng Wang

DOI
https://doi.org/10.1038/s41467-023-38409-5
Journal volume & issue
Vol. 14, no. 1
pp. 1 – 12

Abstract

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Abstract Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank for clinical history and follow-up data. It is still challenging to achieve single cell/nucleus RNA (sc/snRNA) profile in FFPE tissues. Here, we develop a droplet-based snRNA sequencing technology (snRandom-seq) for FFPE tissues by capturing full-length total RNAs with random primers. snRandom-seq shows a minor doublet rate (0.3%), a much higher RNA coverage, and detects more non-coding RNAs and nascent RNAs, compared with state-of-art high-throughput scRNA-seq technologies. snRandom-seq detects a median of >3000 genes per nucleus and identifies 25 typical cell types. Moreover, we apply snRandom-seq on a clinical FFPE human liver cancer specimen and reveal an interesting subpopulation of nuclei with high proliferative activity. Our method provides a powerful snRNA-seq platform for clinical FFPE specimens and promises enormous applications in biomedical research.