ArticlePlant physiology2022
Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles.
Article in Plant physiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 49 citations in OpenAlex.
- Longitudinal zone- and cell type-specific pattern-triggered immune responses in Arabidopsis roots.Developmental cell · 2026Article
- Benchmarking plant single cell RNA-sequencing sample processing strategies.The EMBO journal · 2026Article
- Single-cell and spatial transcriptomics in Phragmites australis reveal the association of B chromosomes with plant invasiveness.Genome biology · 2026Article
- Insights into enhanced, divergent, and additive responses to single and combined hypoxia-salt stress.BMC plant biology · 2026Article
- Single-cell transcriptional profiling in Arabidopsis root exposed to boron toxicity at seedling stages.Plant molecular biology · 2025Article
- A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle.Nature plants · 2025Article
- Single-cell transcriptome sequencing reveals the sphingolipid metabolism pathway plays an important role in leaf senescence in tobacco.BMC plant biology · 2025Article
- 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis.Nature communications · 2025Article
- Dissecting the complexity of local and systemic circadian communication in plants.Npj biological timing and sleep · 2024Review
- Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis.Nature plants · 2024Article
- Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.The Plant cell · 2024Article
- Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology.Biodesign research · 2024Review
- Single-cell transcriptome sequencing of plant leaf expressing anti-HER2 VHH-FcK cancer therapeutic protein.Scientific data · 2023Article
- Transcriptional Landscape of Cotton Roots in Response to Salt Stress at Single-cell Resolution.Plant communications · 2023Article
- Exploring the identity of individual plant cells in space and time.The New phytologist · 2023Review
- Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants.Frontiers in plant science · 2023Review
- Spatially specific mechanisms and functions of the plant circadian clock.Plant physiology · 2022Review
- Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits.International journal of molecular sciences · 2022Review
- Identification of novel regulators required for early development of vein pattern in the cotyledons by single-cell RNA-sequencing.The Plant journal : for cell and molecular biology · 2022Article
- The Plant Cell Atlas: focusing new technologies on the kingdom that nourishes the planet.Plant physiology · 2022Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants' transcriptome substantially changes throughout the day, shaped by the circadian clock, we performed scRNAseq on both Arabidopsis root and above-ground tissues at defined times of the day. For the root scRNAseq analysis, we used tissue-specific reporter lines grown on plates and harvested at the end of the day (ED). In addition, we submitted above-ground tissues from plants grown on soil at ED and end of the night to scRNAseq, which allowed us to identify common cell types/markers between root and shoot and uncover transcriptome changes to above-ground tissues depending on the time of the day. The dataset was also exploited beyond the traditional scRNAseq analysis to investigate non-annotated and di-cistronic transcripts. We experimentally confirmed the predicted presence of some of these transcripts and also addressed the potential function of a previously unidentified marker gene for dividing cells. In summary, this work provides insights into the spatial control of gene expression from nearly 70,000 cells of Arabidopsis for below- and whole above-ground tissue at single-cell resolution at defined time points.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.