Journal Article

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

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

2023

Overview

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. Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank, but single nucleus RNAseq using such tissues is challenging. Here the authors develop a droplet-based method called snRandom-seq for high-throughput and sensitive single nucleus RNA-seq of FFPE samples.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38 / 38/91 / 631/1647/277 / 631/1647/350/877 / 631/61/514/1949 / 692/308/2056 / Bar codes / Droplets / Formaldehyde / Gene Expression Profiling - methods / Gene sequencing / Genomes / Genomics / High-Throughput Nucleotide Sequencing - methods / Hospitals / Humanities and Social Sciences / Humans / Laboratories / Liver cancer / Medical research / Medicine / multidisciplinary / Nuclei / Nuclei (cytology) / Paraffin / Paraffin Embedding - methods / Paraffins / Ribonucleic acid / RNA / RNA - genetics / RNA, Small Nuclear / Science / Science (multidisciplinary) / Sequence Analysis, RNA - methods / snRNA / Tissue Fixation - methods / Tissues