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 () and Yongcheng Wang ()
Additional contact information
Ziye Xu: Zhejiang University School of Medicine
Tianyu Zhang: M20 Genomics
Hongyu Chen: Hangzhou City 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
Yu Chen: Zhejiang University School of Medicine
Jiong Liu: M20 Genomics
Dandan Zhang: Zhejiang University School of Medicine, Hangzhou
Longjiang Fan: Hangzhou City University
Guoji Guo: Zhejiang University Medical Center
Yongcheng Wang: Zhejiang University School of Medicine

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-38409-5

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