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Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos
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 rea...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135740/ https://www.ncbi.nlm.nih.gov/pubmed/30267678 http://dx.doi.org/10.1016/j.isci.2018.08.009 |
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author | Biase, Fernando H. Wu, Qiuyang Calandrelli, Riccardo Rivas-Astroza, Marcelo Zhou, Shuigeng Chen, Zhen Zhong, Sheng |
author_facet | Biase, Fernando H. Wu, Qiuyang Calandrelli, Riccardo Rivas-Astroza, Marcelo Zhou, Shuigeng Chen, Zhen Zhong, Sheng |
author_sort | Biase, Fernando H. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6135740 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-61357402018-09-17 Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos Biase, Fernando H. Wu, Qiuyang Calandrelli, Riccardo Rivas-Astroza, Marcelo Zhou, Shuigeng Chen, Zhen Zhong, Sheng iScience Article 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. Elsevier 2018-08-16 /pmc/articles/PMC6135740/ /pubmed/30267678 http://dx.doi.org/10.1016/j.isci.2018.08.009 Text en © 2018 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Biase, Fernando H. Wu, Qiuyang Calandrelli, Riccardo Rivas-Astroza, Marcelo Zhou, Shuigeng Chen, Zhen Zhong, Sheng Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos |
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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135740/ https://www.ncbi.nlm.nih.gov/pubmed/30267678 http://dx.doi.org/10.1016/j.isci.2018.08.009 |
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