MF-PENS: An Efficient and Versatile Nuclear Extraction Method for Plant Single-Cell Sequencing
Kang, J.; Du, L.; Chen, X.; Liu, Q.; Zhao, M.; Liu, F.; Song, Y.; Zhao, S.; Sun, X.; Tong, C.; Zhang, M.; Liang, Z.; Chen, R.; Yue, Z.
Show abstract
The widespread adoption of single-cell transcriptomics in plants remains constrained by the challenges of isolating high-quality nuclei from tissues with rigid cell walls and complex metabolomes. Here, we present methanol fixation and Percoll-enriched nuclei sorting (MF-PENS), a robust strategy designed to tackle these limitations. Distinct from conventional protocols, MF-PENS circumvents the need for fluorescence activated cell sorting (FACS) and effectively reduce RNA leakage, consistently yielding high-quality single-nucleus RNA sequencing (snRNA-seq) data. MF-PENS has been validated across various plant tissues, including fresh and frozen rice roots and leaves, as well as recalcitrant samples such as soybean root nodules, soybean seeds, and tomato fruits. Benchmarking results demonstrate that MF-PENS significantly enhances gene capture efficiency, cell clustering performance, and cell type annotation accuracy. With its broad applicability and superior performance, MF-PENS represents a robust and versatile tool for plant single-cell research, facilitating deeper insights into plant development and biology processes.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- A Day in the Life of Arabidopsis: 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms 95%
- Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis 95%
- Chemical Imaging Reveals Diverse Functions of Tricarboxylic Acid Metabolites in Root Growth and Development 95%
Similar papers in this journal
- Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development 95%
- The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth 95%
- Comparative transcriptomics in ferns reveals key innovations and divergent evolution of secondary cell wall 95%
Similar papers in this journal
- NanoLoop: A deep learning framework leveraging Nanopore sequencing for chromatin loop prediction 92%
- DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells 92%
- Longitudinal single-cell chemical imaging of engineered strains reveals heterogeneity in fatty acid production 92%
Similar papers in this journal
- Unique and distinct identities and functions of leaf phloem cells revealed by single cell transcriptomics 95%
- Phase separation-based visualization of protein-protein interactions and kinase activities in plants 94%
- Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.