FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants
Abstract The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA prof...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-02-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-021-02288-0 |
| _version_ | 1819173730960539648 |
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| author | Yanping Long Zhijian Liu Jinbu Jia Weipeng Mo Liang Fang Dongdong Lu Bo Liu Hong Zhang Wei Chen Jixian Zhai |
| author_facet | Yanping Long Zhijian Liu Jinbu Jia Weipeng Mo Liang Fang Dongdong Lu Bo Liu Hong Zhang Wei Chen Jixian Zhai |
| author_sort | Yanping Long |
| collection | DOAJ |
| description | Abstract The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities. |
| first_indexed | 2024-12-22T20:27:44Z |
| format | Article |
| id | doaj.art-5ddd059859ae4f2dbb6e0b1fccc89460 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-22T20:27:44Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-5ddd059859ae4f2dbb6e0b1fccc894602022-12-21T18:13:40ZengBMCGenome Biology1474-760X2021-02-0122111410.1186/s13059-021-02288-0FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plantsYanping Long0Zhijian Liu1Jinbu Jia2Weipeng Mo3Liang Fang4Dongdong Lu5Bo Liu6Hong Zhang7Wei Chen8Jixian Zhai9Department of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyDepartment of Biology, School of Life Sciences, Southern University of Science and TechnologyAbstract The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities.https://doi.org/10.1186/s13059-021-02288-0Nanopore sequencingSingle-nucleus RNA-seqLong-read |
| spellingShingle | Yanping Long Zhijian Liu Jinbu Jia Weipeng Mo Liang Fang Dongdong Lu Bo Liu Hong Zhang Wei Chen Jixian Zhai FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants Genome Biology Nanopore sequencing Single-nucleus RNA-seq Long-read |
| title | FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants |
| title_full | FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants |
| title_fullStr | FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants |
| title_full_unstemmed | FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants |
| title_short | FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants |
| title_sort | flsnrna seq protoplasting free full length single nucleus rna profiling in plants |
| topic | Nanopore sequencing Single-nucleus RNA-seq Long-read |
| url | https://doi.org/10.1186/s13059-021-02288-0 |
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