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

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 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.

Язык: Английский

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

и другие.

Nature Plants, Год журнала: 2025, Номер unknown

Опубликована: Фев. 25, 2025

Язык: Английский

Процитировано

2
Single-Cell Transcriptomics Applied in Plants DOI Creative Commons
Yanyan Sun, Jian Sun,

Chunjing Lin

и другие.

Cells, Год журнала: 2024, Номер 13(18), С. 1561 - 1561

Опубликована: Сен. 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.

Язык: Английский

Процитировано

3
Decoding maize meristems maintenance and differentiation: integrating single-cell and spatial omics DOI
Bin Li, Wenhao Liu, Jie Xu

и другие.

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

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

Bogun Park

и другие.

Plant Biotechnology Reports, Год журнала: 2025, Номер unknown

Опубликована: Апрель 3, 2025

Язык: Английский

Процитировано

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

Current Opinion in Plant Biology, Год журнала: 2025, Номер 85, С. 102726 - 102726

Опубликована: Апрель 24, 2025

Язык: Английский

Процитировано

0
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, Год журнала: 2024, Номер 82, С. 102662 - 102662

Опубликована: Ноя. 13, 2024

Язык: Английский

Процитировано

1
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

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 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.

Язык: Английский

Процитировано

0