Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos

Summary: We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker gene...

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Main Authors:	Fernando H. Biase, Qiuyang Wu, Riccardo Calandrelli, Marcelo Rivas-Astroza, Shuigeng Zhou, Zhen Chen, Sheng Zhong
Format:	Article
Language:	English
Published:	Elsevier 2018-09-01
Series:	iScience
Online Access:	http://www.sciencedirect.com/science/article/pii/S2589004218301214

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spelling	doaj-a4259878bc1845e4beef5bdd51d2ff872020-11-24T23:20:33ZengElsevieriScience2589-00422018-09-0171629Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation EmbryosFernando H. Biase0Qiuyang Wu1Riccardo Calandrelli2Marcelo Rivas-Astroza3Shuigeng Zhou4Zhen Chen5Sheng Zhong6Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USADepartment of Bioengineering, University of California San Diego, San Diego, CA 92130, USA; Department of Computer Science and Technology, Tongji University, Shanghai 201804, ChinaDepartment of Bioengineering, University of California San Diego, San Diego, CA 92130, USADepartment of Bioengineering, University of California San Diego, San Diego, CA 92130, USASchool of Computer Science, Fudan University, Shanghai 200433, ChinaDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USADepartment of Bioengineering, University of California San Diego, San Diego, CA 92130, USA; Corresponding authorSummary: We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell transcriptomes. We triggered lineage tracking in each blastomere at the 2-cell stage, observed microscopically inequivalent contributions of the progeny to the two embryonic poles at the blastocyst stage, and analyzed every single cell at either 4- or 8-cell stage with deep paired-end sequencing of full-length transcripts. Although lineage difference was not marked unequivocally at a single-gene level, it became clear when the transcriptome was analyzed as a whole. Moreover, several groups of novel transcript isoforms with embedded repeat sequences exhibited lineage difference, suggesting a possible link between DNA demethylation and cell fate decision. Rainbow-seq bridged a critical gap between division history and single-cell RNA-seq assays. : Preimplantation, Cell fate, Single cell, Lineage tracing, Transposon Subject Areas: Preimplantation, Cell fate, Single cell, Lineage tracing, Transposonhttp://www.sciencedirect.com/science/article/pii/S2589004218301214
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Fernando H. Biase Qiuyang Wu Riccardo Calandrelli Marcelo Rivas-Astroza Shuigeng Zhou Zhen Chen Sheng Zhong
spellingShingle	Fernando H. Biase Qiuyang Wu Riccardo Calandrelli Marcelo Rivas-Astroza Shuigeng Zhou Zhen Chen Sheng Zhong Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos iScience
author_facet	Fernando H. Biase Qiuyang Wu Riccardo Calandrelli Marcelo Rivas-Astroza Shuigeng Zhou Zhen Chen Sheng Zhong
author_sort	Fernando H. Biase
title	Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos
title_short	Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos
title_full	Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos
title_fullStr	Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos
title_full_unstemmed	Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos
title_sort	rainbow-seq: combining cell lineage tracing with single-cell rna sequencing in preimplantation embryos
publisher	Elsevier
series	iScience
issn	2589-0042
publishDate	2018-09-01
description	Summary: We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell transcriptomes. We triggered lineage tracking in each blastomere at the 2-cell stage, observed microscopically inequivalent contributions of the progeny to the two embryonic poles at the blastocyst stage, and analyzed every single cell at either 4- or 8-cell stage with deep paired-end sequencing of full-length transcripts. Although lineage difference was not marked unequivocally at a single-gene level, it became clear when the transcriptome was analyzed as a whole. Moreover, several groups of novel transcript isoforms with embedded repeat sequences exhibited lineage difference, suggesting a possible link between DNA demethylation and cell fate decision. Rainbow-seq bridged a critical gap between division history and single-cell RNA-seq assays. : Preimplantation, Cell fate, Single cell, Lineage tracing, Transposon Subject Areas: Preimplantation, Cell fate, Single cell, Lineage tracing, Transposon
url	http://www.sciencedirect.com/science/article/pii/S2589004218301214
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Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos

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