FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing

Yun Li; Zheng Huang; Zhaojun Zhang; Qifei Wang; Fengxian Li; Shufang Wang; Xin Ji; Shaokun Shu; Xiangdong Fang; Lan Jiang

doi:10.1186/s13059-023-02893-1

FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing

Genome Biol. 2023 Apr 6;24(1):70. doi: 10.1186/s13059-023-02893-1.

Authors

Yun Li^#^{1

2

3}, Zheng Huang^#^{1

2

3}, Zhaojun Zhang^#^{1

2

3

4}, Qifei Wang^{1

2

3}, Fengxian Li⁵, Shufang Wang⁵, Xin Ji⁶, Shaokun Shu⁷, Xiangdong Fang^{1

2

3

8

9}, Lan Jiang^{10

11

12

13

14

15}

Affiliations

¹ China National Center for Bioinformation, Beijing, 100101, China.
² CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
³ University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China.
⁵ The Blood Transfusion Department, First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China.
⁶ Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing, 100142, China.
⁷ Peking University International Cancer Institute & Peking University Cancer Hospital & Institute, Beijing, 100191, China.
⁸ Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
⁹ Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
¹⁰ China National Center for Bioinformation, Beijing, 100101, China. jiangl@big.ac.cn.
¹¹ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. jiangl@big.ac.cn.
¹² University of Chinese Academy of Sciences, Beijing, 100049, China. jiangl@big.ac.cn.
¹³ Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China. jiangl@big.ac.cn.
¹⁴ Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China. jiangl@big.ac.cn.
¹⁵ College of Future Technology College, University of Chinese Academy of Sciences, Beijing, 100049, China. jiangl@big.ac.cn.

^# Contributed equally.

Abstract

Single-cell RNA sequencing methods focusing on the 5'-end of transcripts can reveal promoter and enhancer activity and efficiently profile immune receptor repertoire. However, ultra-high-throughput 5'-end single-cell RNA sequencing methods have not been described. We introduce FIPRESCI, 5'-end single-cell combinatorial indexing RNA-Seq, enabling massive sample multiplexing and increasing the throughput of the droplet microfluidics system by over tenfold. We demonstrate FIPRESCI enables the generation of approximately 100,000 single-cell transcriptomes from E10.5 whole mouse embryos in a single-channel experiment, and simultaneous identification of subpopulation differences and T cell receptor signatures of peripheral blood T cells from 12 cancer patients.

Keywords: 10X Genomics; Combinatorial indexing; Sample multiplexing; Single-cell RNA-seq; Single-nucleus RNA-seq; scTCR-seq; scVDJ-seq.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
High-Throughput Nucleotide Sequencing
Mice
Microfluidics* / methods
RNA / genetics
Sequence Analysis, RNA / methods
Single-Cell Analysis* / methods
Transcriptome

Substances

RNA