| Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish |
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| 作者姓名： | Chang Ye Zhuoxin Chen Zhan Liu Feng Wang Xionglei He |
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| 作者单位： | State Key Laboratory of Biocontrol |
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| 基金项目： | We are grateful to J.Huang and Z.Zhang for technical support.This work was supported by a grant from the National Key Program of China(2017YFA0103504 to X.H.)。 |
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| 摘 要： | There is a growing interest in developing experimental methods for tracking the developmental cell lineages of a complex organism.The recently developed CRISPR/Cas9-based barcoding method is,although highly promising,difficult to scale up because it relies on exogenous barcoding sequences that are engineered into the genome.In this study,we characterized 78 high-quality endogenous sites in the zebrafish genome that can be used as CRISPR/Cas9-based barcoding sites.The 78 sites are all highly expressed in most of the cell types according to single-cell RNA sequencing(scRNA-seq)data.Hence,the barcoding information of the 78 endogenous sites is recovered by the available scRNA-seq platforms,enabling simultaneous characterization of cell type and cell lineage information.
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| 关 键 词： | ZEBRAFISH CRISPR/Cas9 Cell LINEAGE Development SINGLE-CELL RNA sequencing |
| 收稿时间： | 29 July 2019 |
Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish |
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| Chang Ye,Zhuoxin Chen,Zhan Liu,Feng Wang,Xionglei He.Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish[J].Journal of Genetics and Genomics,2020,47(2):85-91. |
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| Institution: | 1. Blood Bank, Faculty of Medicine, Balcali Hospital, Cukurova University, Saricam, Adana 01330, Turkey;2. Division of Infectious Diseases, Faculty of Medicine, Balcali Hospital, Cukurova University, Saricam, Adana 01330, Turkey;3. Department of Microbiology, Faculty of Medicine, Balcali Hospital, Cukurova University, Saricam, Adana 01330, Turkey;4. Hemapheresis, Stem Cell and Cryopreservation Unit, Balcali Hospital, Cukurova University, Saricam, Adana 01330, Turkey;5. Department of Internal Medicine, Division of Hematology, Balcali Hospital, Cukurova University, Saricam, Adana 01330, Turkey;6. Hisar Intercontinental Hospital, Umraniye, Istanbul 34768, Turkey;1. Department of Statistics, University of Akron, Akron, OH, USA;2. Department of Environmental Health Science, Indiana University-Purdue University, Indianapolis, IN, USA;1. Regional Blood Center, Gulhane Military Academy of Medicine, Ankara, Turkey;2. Department of General Surgery, Gulhane Military Academy of Medicine, Ankara, Turkey;3. Military Hospital, Isparta, Turkey;4. Department of Medical Microbiology, Gulhane Military Academy of Medicine, Ankara, Turkey;5. Department of Infectious Disease and Clinical Microbiology, Gulhane Military Academy of Medicine, Ankara, Turkey;6. Department of Infectious Disease and Clinical Microbiology, Sanko University, Gaziantep, Turkey |
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| Abstract: | There is a growing interest in developing experimental methods for tracking the developmental cell lineages of a complex organism.The recently developed CRISPR/Cas9-based barcoding method is,although highly promising,difficult to scale up because it relies on exogenous barcoding sequences that are engineered into the genome.In this study,we characterized 78 high-quality endogenous sites in the zebrafish genome that can be used as CRISPR/Cas9-based barcoding sites.The 78 sites are all highly expressed in most of the cell types according to single-cell RNA sequencing (scRNA-seq) data.Hence,the barcoding information of the 78 endogenous sites is recovered by the available scRNA-seq platforms,enabling simultaneous characterization of cell type and cell lineage information. |
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| Keywords: | Zebrafish CRISPR/Cas9 Cell lineage Development Single-cell RNA sequencing |
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