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

Author

Listed:
  • Ziye Xu

    (Zhejiang University School of Medicine
    Zhejiang University Medical Center)

  • Tianyu Zhang

    (M20 Genomics)

  • Hongyu Chen

    (Hangzhou City University
    Zhejiang University
    Zhejiang University)

  • Yuyi Zhu

    (Zhejiang University Medical Center)

  • Yuexiao Lv

    (Zhejiang University Medical Center)

  • Shunji Zhang

    (Zhejiang University)

  • Jiaye Chen

    (Harvard Medical School)

  • Haide Chen

    (Zhejiang University Medical Center)

  • Lili Yang

    (Zhejiang University School of Medicine)

  • Weiqin Jiang

    (Zhejiang University)

  • Shengyu Ni

    (M20 Genomics)

  • Fangru Lu

    (M20 Genomics)

  • Zhaolun Wang

    (M20 Genomics)

  • Hao Yang

    (M20 Genomics)

  • Ling Dong

    (M20 Genomics)

  • Feng Chen

    (Zhejiang University School of Medicine)

  • Hong Zhang

    (Zhejiang University
    Zhejiang University School of Medicine)

  • Yu Chen

    (Zhejiang University School of Medicine)

  • Jiong Liu

    (M20 Genomics)

  • Dandan Zhang

    (Zhejiang University School of Medicine, Hangzhou
    Zhejiang University)

  • Longjiang Fan

    (Hangzhou City University
    Zhejiang University
    Zhejiang University)

  • Guoji Guo

    (Zhejiang University Medical Center)

  • Yongcheng Wang

    (Zhejiang University School of Medicine
    Zhejiang University Medical Center
    Zhejiang University)

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.

Suggested Citation

  • 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 C, 2023. "High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38409-5
    DOI: 10.1038/s41467-023-38409-5
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    References listed on IDEAS

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