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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018-09-01
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| Series: | iScience |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004218301214 |
| _version_ | 1819232348169830400 |
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| author | Fernando H. Biase Qiuyang Wu Riccardo Calandrelli Marcelo Rivas-Astroza Shuigeng Zhou Zhen Chen Sheng Zhong |
| author_facet | Fernando H. Biase Qiuyang Wu Riccardo Calandrelli Marcelo Rivas-Astroza Shuigeng Zhou Zhen Chen Sheng Zhong |
| author_sort | Fernando H. Biase |
| collection | DOAJ |
| 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 |
| first_indexed | 2024-12-23T11:59:26Z |
| format | Article |
| id | doaj.art-a4259878bc1845e4beef5bdd51d2ff87 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-23T11:59:26Z |
| publishDate | 2018-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-a4259878bc1845e4beef5bdd51d2ff872022-12-21T17:48:00ZengElsevieriScience2589-00422018-09-0171629Rainbow-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 |
| 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 |
| title | 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_short | 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 |
| url | http://www.sciencedirect.com/science/article/pii/S2589004218301214 |
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