Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation
Recent advances in developmental biology have been made possible by using multi-omic studies at single cell resolution. However, progress in plants has been slowed, owing to the tremendous difficulty in protoplast isolation from most plant tissues and/or oversize protoplasts during flow cytometry pu...
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MDPI AG
2022-12-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/11/23/3919 |
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| author | Ming-Chao Yang Zi-Chen Wu Liang-Liang Huang Farhat Abbas Hui-Cong Wang |
| author_facet | Ming-Chao Yang Zi-Chen Wu Liang-Liang Huang Farhat Abbas Hui-Cong Wang |
| author_sort | Ming-Chao Yang |
| collection | DOAJ |
| description | Recent advances in developmental biology have been made possible by using multi-omic studies at single cell resolution. However, progress in plants has been slowed, owing to the tremendous difficulty in protoplast isolation from most plant tissues and/or oversize protoplasts during flow cytometry purification. Surprisingly, rapid innovations in nucleus research have shed light on plant studies in single cell resolution, which necessitates high quality and efficient nucleus isolation. Herein, we present efficient nuclei isolation protocols from the leaves of ten important plants including <i>Arabidopsis</i>, rice, maize, tomato, soybean, banana, grape, citrus, apple, and litchi. We provide a detailed procedure for nucleus isolation, flow cytometry purification, and absolute nucleus number quantification. The nucleus isolation buffer formula of the ten plants tested was optimized, and the results indicated a high nuclei yield. Microscope observations revealed high purity after flow cytometry sorting, and the DNA and RNA quality extract from isolated nuclei were monitored by using the nuclei in cell division cycle and single nucleus RNA sequencing (snRNA-seq) studies, with detailed procedures provided. The findings indicated that nucleus yield and quality meet the requirements of snRNA-seq, cell division cycle, and likely other omic studies. The protocol outlined here makes it feasible to perform plant omic studies at single cell resolution. |
| first_indexed | 2024-03-09T17:50:42Z |
| format | Article |
| id | doaj.art-b7015c0f82954aa3a1212a41727f0d42 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-09T17:50:42Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-b7015c0f82954aa3a1212a41727f0d422023-11-24T10:46:00ZengMDPI AGCells2073-44092022-12-011123391910.3390/cells11233919Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics InterrogationMing-Chao Yang0Zi-Chen Wu1Liang-Liang Huang2Farhat Abbas3Hui-Cong Wang4Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaBecton Dickinson Medical Devices (Shanghai) Co., Ltd., Guangzhou 510180, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaRecent advances in developmental biology have been made possible by using multi-omic studies at single cell resolution. However, progress in plants has been slowed, owing to the tremendous difficulty in protoplast isolation from most plant tissues and/or oversize protoplasts during flow cytometry purification. Surprisingly, rapid innovations in nucleus research have shed light on plant studies in single cell resolution, which necessitates high quality and efficient nucleus isolation. Herein, we present efficient nuclei isolation protocols from the leaves of ten important plants including <i>Arabidopsis</i>, rice, maize, tomato, soybean, banana, grape, citrus, apple, and litchi. We provide a detailed procedure for nucleus isolation, flow cytometry purification, and absolute nucleus number quantification. The nucleus isolation buffer formula of the ten plants tested was optimized, and the results indicated a high nuclei yield. Microscope observations revealed high purity after flow cytometry sorting, and the DNA and RNA quality extract from isolated nuclei were monitored by using the nuclei in cell division cycle and single nucleus RNA sequencing (snRNA-seq) studies, with detailed procedures provided. The findings indicated that nucleus yield and quality meet the requirements of snRNA-seq, cell division cycle, and likely other omic studies. The protocol outlined here makes it feasible to perform plant omic studies at single cell resolution.https://www.mdpi.com/2073-4409/11/23/3919nucleus isolationplantscell division cyclingsingle nucleus RNA sequencing |
| spellingShingle | Ming-Chao Yang Zi-Chen Wu Liang-Liang Huang Farhat Abbas Hui-Cong Wang Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation Cells nucleus isolation plants cell division cycling single nucleus RNA sequencing |
| title | Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation |
| title_full | Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation |
| title_fullStr | Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation |
| title_full_unstemmed | Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation |
| title_short | Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation |
| title_sort | systematic methods for isolating high purity nuclei from ten important plants for omics interrogation |
| topic | nucleus isolation plants cell division cycling single nucleus RNA sequencing |
| url | https://www.mdpi.com/2073-4409/11/23/3919 |
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