we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes.A total of 24 putative cell clusters and the cluster-specific marker genes were identified.The spatial distribution and temporal ordering of the individual cells at different developmental stages illustrate their...
While recent advances in plant single-cell RNA sequencing (scRNA-seq) have made numerous strides in identifying novel regulatory events, transcriptional profiling of certain cell types, such as phloem poles, has not yet been thoroughly investigated. A recent article by Otero et al. utilized cell-t...
Here, we harmonized single cell mRNA sequencing data from over 110,000 cells to construct a comprehensive atlas for a stereotypically developing organ with indeterminate growth, the Arabidopsis root. To test the utility of the atlas to interpret new datasets, we profiled mutants for two key ...
Recent genome-wide analyses of transcription with scRNA-seq data also provide a new picture of the molecular basis of gene expression regulation for different cell types in plant response to stress35. Therefore, further understanding of maize root responses to temperature at the cell type will be ...
High-throughput single-cellRNA sequencing (scRNAseq) is becoming a cornerstone of developmental research, providing unprecedented power in understanding dynamic processes. Here, we present a high-resolution scRNA-seq expression atlas of the Arabidopsis root composed of thousands of independently profiled ...
AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and...
Integrated analysis of scRNA and bulk RNA-seq data revealed aberrant expression of Epidermis cell subpopulations in flooding, Pi, and salt stresses. Conclusion Taken together, our results demonstrate that NRTPredictor is a useful tool for automated prediction of rice root cell stage and provides a ...
RNA-seq have been described. These methods work in one of two ways. Single cells can be isolated with a micromanipulator or into droplets (Imdahl et al., 2020;Ma et al., 2021;McNulty et al., 2023;Sheng et al., 2017;Shi et al., 2013). The cDNA from each single cell is then ...
A python package to compute E-distances in single-cell perturbation data and perform E-tests. Please note that maintenance on the scperturb Python package is relatively slow. We have recreated Python functionality inpertpywhich has a larger base of support and also includes fast calculation of al...
Establishing legume–rhizobial symbiosis requires precise coordination of complex responses in a time- and cell type-specific manner. Encountering Rhizobium, rapid changes of gene expression levels in host plants occur in the first few hours, which prepa