Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis DOI Creative Commons
Jie Yao, Nianmin Shang, Hongyu Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Abstract Single-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function development. However, plant cell’s rigid walls require protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq various tissues before after protoplasting. Cell-type specific effects were discovered in different tissues. Protoplasting-related biases found to distort clustering, marker identification, multi-omics integration. By calculating protoplasted scores based expression, identified mitigated effects, enabling the accurate clustering annotation tobacco BY-2 cells identification cell-cycle-related genes. Our findings underscore importance assessing correcting analysis, offering new insights more interpretation biological discovery.

Language: Английский

MicroRNA control of stem cell reconstitution and growth in root regeneration DOI
Julia L. Baulies, Ramiro E. Rodríguez, Franco E Lazzara

et al.

Nature Plants, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

Language: Английский

Citations

2
Decoding maize meristems maintenance and differentiation: integrating single-cell and spatial omics DOI
Bin Li, Wenhao Liu, Jie Xu

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

0
Recent progress in single-cell transcriptomic studies in plants DOI Creative Commons
Yuhan Cho, Ulhas Sopanrao Kadam,

Bogun Park

et al.

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

Citations

0
Coordination and regulation of vascular development in roots DOI Creative Commons
Yuki Kondo, Kyoko Ohashi‐Ito

Current Opinion in Plant Biology, Journal Year: 2025, Volume and Issue: 85, P. 102726 - 102726

Published: April 24, 2025

Language: Английский

Citations

0
Single-Cell Transcriptomics Applied in Plants DOI Creative Commons
Yanyan Sun, Jian Sun,

Chunjing Lin

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(18), P. 1561 - 1561

Published: Sept. 17, 2024

Single-cell RNA sequencing (scRNA-seq) is a high-tech method for characterizing the expression patterns of heterogeneous cells in same tissue and has changed our evaluation biological systems by increasing number individual analyzed. However, full potential scRNA-seq, particularly plant science, not yet been elucidated. To explore utilization scRNA-seq technology plants, we firstly conducted comprehensive review significant findings past few years. Secondly, introduced research applications to tissues recent years, primarily focusing on model crops, wood. We then offered five databases that could facilitate identification distinct marker genes various cell types. Finally, analyzed problems, challenges, directions applying with aim providing theoretical foundation better use this technique future research.

Language: Английский

Citations

3
Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities DOI
Mukesh Jain

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102662 - 102662

Published: Nov. 13, 2024

Language: Английский

Citations

0
Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis DOI Creative Commons
Jie Yao, Nianmin Shang, Hongyu Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Abstract Single-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function development. However, plant cell’s rigid walls require protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq various tissues before after protoplasting. Cell-type specific effects were discovered in different tissues. Protoplasting-related biases found to distort clustering, marker identification, multi-omics integration. By calculating protoplasted scores based expression, identified mitigated effects, enabling the accurate clustering annotation tobacco BY-2 cells identification cell-cycle-related genes. Our findings underscore importance assessing correcting analysis, offering new insights more interpretation biological discovery.

Language: Английский

Citations

0