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

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′-...
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Autor*in:	Li, Yun [verfasserIn] Huang, Zheng Zhang, Zhaojun Wang, Qifei Li, Fengxian Wang, Shufang Ji, Xin Shu, Shaokun Fang, Xiangdong Jiang, Lan

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

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

Anmerkung:	© The Author(s) 2023. corrected publication 2023

Übergeordnetes Werk:	Enthalten in: Genome biology - London : BioMed Central, 2000, 24(2023), 1 vom: 06. Apr.
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:1 ; day:06 ; month:04

Links:	Volltext

DOI / URN:	10.1186/s13059-023-02893-1

Katalog-ID:	SPR049971948

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520			\|a 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.
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allfields	10.1186/s13059-023-02893-1 doi (DE-627)SPR049971948 (SPR)s13059-023-02893-1-e DE-627 ger DE-627 rakwb eng Li, Yun verfasserin aut FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023. corrected publication 2023 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. Combinatorial indexing (dpeaa)DE-He213 Sample multiplexing (dpeaa)DE-He213 Single-cell RNA-seq (dpeaa)DE-He213 Single-nucleus RNA-seq (dpeaa)DE-He213 scVDJ-seq (dpeaa)DE-He213 scTCR-seq (dpeaa)DE-He213 10X Genomics (dpeaa)DE-He213 Huang, Zheng aut Zhang, Zhaojun aut Wang, Qifei aut Li, Fengxian aut Wang, Shufang aut Ji, Xin aut Shu, Shaokun aut Fang, Xiangdong aut Jiang, Lan (orcid)0000-0003-2008-9631 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02893-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 06 04
spelling	10.1186/s13059-023-02893-1 doi (DE-627)SPR049971948 (SPR)s13059-023-02893-1-e DE-627 ger DE-627 rakwb eng Li, Yun verfasserin aut FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023. corrected publication 2023 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. Combinatorial indexing (dpeaa)DE-He213 Sample multiplexing (dpeaa)DE-He213 Single-cell RNA-seq (dpeaa)DE-He213 Single-nucleus RNA-seq (dpeaa)DE-He213 scVDJ-seq (dpeaa)DE-He213 scTCR-seq (dpeaa)DE-He213 10X Genomics (dpeaa)DE-He213 Huang, Zheng aut Zhang, Zhaojun aut Wang, Qifei aut Li, Fengxian aut Wang, Shufang aut Ji, Xin aut Shu, Shaokun aut Fang, Xiangdong aut Jiang, Lan (orcid)0000-0003-2008-9631 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02893-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 06 04
allfields_unstemmed	10.1186/s13059-023-02893-1 doi (DE-627)SPR049971948 (SPR)s13059-023-02893-1-e DE-627 ger DE-627 rakwb eng Li, Yun verfasserin aut FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023. corrected publication 2023 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. Combinatorial indexing (dpeaa)DE-He213 Sample multiplexing (dpeaa)DE-He213 Single-cell RNA-seq (dpeaa)DE-He213 Single-nucleus RNA-seq (dpeaa)DE-He213 scVDJ-seq (dpeaa)DE-He213 scTCR-seq (dpeaa)DE-He213 10X Genomics (dpeaa)DE-He213 Huang, Zheng aut Zhang, Zhaojun aut Wang, Qifei aut Li, Fengxian aut Wang, Shufang aut Ji, Xin aut Shu, Shaokun aut Fang, Xiangdong aut Jiang, Lan (orcid)0000-0003-2008-9631 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02893-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 06 04
allfieldsGer	10.1186/s13059-023-02893-1 doi (DE-627)SPR049971948 (SPR)s13059-023-02893-1-e DE-627 ger DE-627 rakwb eng Li, Yun verfasserin aut FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023. corrected publication 2023 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. Combinatorial indexing (dpeaa)DE-He213 Sample multiplexing (dpeaa)DE-He213 Single-cell RNA-seq (dpeaa)DE-He213 Single-nucleus RNA-seq (dpeaa)DE-He213 scVDJ-seq (dpeaa)DE-He213 scTCR-seq (dpeaa)DE-He213 10X Genomics (dpeaa)DE-He213 Huang, Zheng aut Zhang, Zhaojun aut Wang, Qifei aut Li, Fengxian aut Wang, Shufang aut Ji, Xin aut Shu, Shaokun aut Fang, Xiangdong aut Jiang, Lan (orcid)0000-0003-2008-9631 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02893-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 06 04
allfieldsSound	10.1186/s13059-023-02893-1 doi (DE-627)SPR049971948 (SPR)s13059-023-02893-1-e DE-627 ger DE-627 rakwb eng Li, Yun verfasserin aut FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023. corrected publication 2023 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. Combinatorial indexing (dpeaa)DE-He213 Sample multiplexing (dpeaa)DE-He213 Single-cell RNA-seq (dpeaa)DE-He213 Single-nucleus RNA-seq (dpeaa)DE-He213 scVDJ-seq (dpeaa)DE-He213 scTCR-seq (dpeaa)DE-He213 10X Genomics (dpeaa)DE-He213 Huang, Zheng aut Zhang, Zhaojun aut Wang, Qifei aut Li, Fengxian aut Wang, Shufang aut Ji, Xin aut Shu, Shaokun aut Fang, Xiangdong aut Jiang, Lan (orcid)0000-0003-2008-9631 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02893-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 06 04
language	English
source	Enthalten in Genome biology 24(2023), 1 vom: 06. Apr. volume:24 year:2023 number:1 day:06 month:04
sourceStr	Enthalten in Genome biology 24(2023), 1 vom: 06. Apr. volume:24 year:2023 number:1 day:06 month:04
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institution	findex.gbv.de
topic_facet	Combinatorial indexing Sample multiplexing Single-cell RNA-seq Single-nucleus RNA-seq scVDJ-seq scTCR-seq 10X Genomics
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container_title	Genome biology
authorswithroles_txt_mv	Li, Yun @@aut@@ Huang, Zheng @@aut@@ Zhang, Zhaojun @@aut@@ Wang, Qifei @@aut@@ Li, Fengxian @@aut@@ Wang, Shufang @@aut@@ Ji, Xin @@aut@@ Shu, Shaokun @@aut@@ Fang, Xiangdong @@aut@@ Jiang, Lan @@aut@@
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author	Li, Yun
spellingShingle	Li, Yun misc Combinatorial indexing misc Sample multiplexing misc Single-cell RNA-seq misc Single-nucleus RNA-seq misc scVDJ-seq misc scTCR-seq misc 10X Genomics FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing
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topic_title	FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing Combinatorial indexing (dpeaa)DE-He213 Sample multiplexing (dpeaa)DE-He213 Single-cell RNA-seq (dpeaa)DE-He213 Single-nucleus RNA-seq (dpeaa)DE-He213 scVDJ-seq (dpeaa)DE-He213 scTCR-seq (dpeaa)DE-He213 10X Genomics (dpeaa)DE-He213
topic	misc Combinatorial indexing misc Sample multiplexing misc Single-cell RNA-seq misc Single-nucleus RNA-seq misc scVDJ-seq misc scTCR-seq misc 10X Genomics
topic_unstemmed	misc Combinatorial indexing misc Sample multiplexing misc Single-cell RNA-seq misc Single-nucleus RNA-seq misc scVDJ-seq misc scTCR-seq misc 10X Genomics
topic_browse	misc Combinatorial indexing misc Sample multiplexing misc Single-cell RNA-seq misc Single-nucleus RNA-seq misc scVDJ-seq misc scTCR-seq misc 10X Genomics
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title	FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing
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title_full	FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing
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title_sort	fipresci: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell rna sequencing
title_auth	FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing
abstract	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. © The Author(s) 2023. corrected publication 2023
abstractGer	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. © The Author(s) 2023. corrected publication 2023
abstract_unstemmed	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. © The Author(s) 2023. corrected publication 2023
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title_short	FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing
url	https://dx.doi.org/10.1186/s13059-023-02893-1
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author2	Huang, Zheng Zhang, Zhaojun Wang, Qifei Li, Fengxian Wang, Shufang Ji, Xin Shu, Shaokun Fang, Xiangdong Jiang, Lan
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FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5′-end single-cell RNA sequencing

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