References
Public datasets used by PlantscRNAdb
Arabidopsis thaliana
Totally 33 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA506007 | High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types Authors: Shulse et al., Publication Date: 2019.05.14 Journal: Cell Reports DOI: 10.1016/j.celrep.2019.04.054 Protocol: Drop-seq Tissues: Root No. Cells: >12,000 |
| PRJNA471914 | Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation Authors: Turco et al., Publication Date: 2019.07.09 Journal: Cell Reports DOI: 10.1016/j.celrep.2019.06.041 Protocol: Drop-seq Tissues: Root No. Cells: 374 |
| PRJNA551314 | A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing Authors: Torii et al., Publication Date: 2022.07.12 Journal: Cell Reports DOI: 10.1016/j.celrep.2022.111059 Protocol: cpRNA-seq Tissues: Cotyledon No. Cells: |
| PRJNA835893 | Single-nucleus RNA-seq reveals that MBD5, MBD6,and SILENZIO maintain silencing in the vegetativecell of developing pollen Authors: Ichino et al., Publication Date: 2022.11.20 Journal: Cell Reports DOI: 10.1016/j.celrep.2022.111699 Protocol: 10x Genomics Tissues: Developing male gametophytes No. Cells: / |
| PRJNA509920 | Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing Authors: Denyer et al., Publication Date: 2019.03.25 Journal: Developmental Cell DOI: 10.1016/j.devcel.2019.02.022 Protocol: 10x Genomics Tissues: Root No. Cells: 4,727 |
| PRJCA003094 | A single-cell analysis of the Arabidopsis vegetative shoot apex Authors: Zhang et al., Publication Date: 2021.03.15 Journal: Developmetnal Cell DOI: 10.1016/j.devcel.2021.02.021 Protocol: 10x Genomics Tissues: Vegetative shoot apex No. Cells: 36,643 |
| PRJNA640389 | A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants Authors: Shahan et al., Publication Date: 2020.06.29 Journal: Developmental Cell DOI: 10.1016/j.devcel.2022.01.008 Protocol: 10x Genomics Tissues: Root No. Cells: 110,000 |
| PRJNA517021 | A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root Authors: Zhang et al., Publication Date: 2019.05.06 Journal: Molecular Plant DOI: 10.1016/j.molp.2019.04.004 Protocol: 10x Genomics Tissues: Root No. Cells: 8,000 |
| PRJNA577177 | Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing Authors: Liu et al., Publication Date: 2020.08.03 Journal: Molecular Plant DOI: 10.1016/j.molp.2020.06.010 Protocol: 10x Genomics Tissues: Cotyledon No. Cells: 12,844 |
| PRJNA649267 | Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level Authors: Farmer et al., Publication Date: 2021.01.05 Journal: Molecular Plant DOI: 10.1016/j.molp.2021.01.001 Protocol: 10x Genomics(scRNA+scATAC) Tissues: Root No. Cells: 10,548 |
| PRJNA680241 | Reconstruction of Lateral Root Formation Through Single-Cell RNA-seq Reveals Order of Tissue Initiation Authors: Serrano-Ron et al., Publication Date: 2021.05.28 Journal: Molecular Plant DOI: 10.1016/j.molp.2021.05.028 Protocol: Smart-seq2 Tissues: Lateral root No. Cells: 282 |
| PRJNA750934 | A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root Authors: Graeff et al., Publication Date: 2021.08.03 Journal: Molecular Plant DOI: 10.1016/j.molp.2021.07.021 Protocol: 10x Genomics Tissues: Root No. Cells: 12,491 |
| PRJNA613684 | Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses Authors: Liu et al., Publication Date: 2021.04.03 Journal: Plant communication DOI: 10.1016/j.xplc.2022.100306 Protocol: 10x Genomics Tissues: Leaf No. Cells: 7,225 |
| PRJNA659737 | Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration Authors: Zhai et al., Publication Date: 2021.11.07 Journal: Nature Plant DOI: 10.1038/s41477-021-01015-8 Protocol: BD Rhapsody system Tissues: Root callus No. Cells: 5,913 |
| PRJEB47244 | High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana Authors: Hou et al., Publication Date: 2021.10.01 Journal: Communications Biology DOI: 10.1038/s42003-021-02676-z Protocol: 10x Genomics Tissues: Ovule primordia No. Cells: 16,872 |
| PRJNA678377 | Distinct identities of leaf phloem cells revealed by single cell transcriptomics Authors: Kim et al., Publication Date: 2021.01.14 Journal: The Plant Cell DOI: 10.1093/plcell/koaa060 Protocol: 10x Genomics Tissues: Leaf No. Cells: 5,230 |
| PRJNA764868 | Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection Authors: Procko et al., Publication Date: 2022.08.25 Journal: The Plant Cell DOI: 10.1093/plcell/koac167 Protocol: 10x Genomics Tissues: Leaf No. Cells: 23729 |
| E-MTAB-11006 | Single-cell transcriptomics sheds light on the identityand metabolism of developing leaf cells Authors: Berrio et al., Publication Date: 2021.10.123 Journal: Plant Physiology DOI: 10.1093/plphys/kiab489 Protocol: 10x Genomics Tissues: Seedling No. Cells: 1,800 |
| PRJNA742744 | Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles Authors: Apelt et al., Publication Date: 2021.11.19 Journal: Plant Physiology DOI: 10.1093/plphys/kiab537 Protocol: Drop-seq Tissues: Shoot, root No. Cells: / |
| PRJNA660263 | Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution Authors: Picard et al., Publication Date: 2021.05.31 Journal: Nature Plant DOI: 10.1101/2020.08.25.267476 Protocol: Smart-seq2 Tissues: Seed No. Cells: 1,437 |
| PRJNA703045 | Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf Authors: Lopez-Anido et al., Publication Date: 2020.09.08 Journal: Developmental Cell DOI: 10.1101/2020.09.08.288498 Protocol: 10x Genomics & Smart-seq2 Tissues: Whole aerial tissue or first true leaves No. Cells: 18,000 |
| PRJNA666436 | A single cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana Authors: Gala et al., Publication Date: 2020.10.02 Journal: The Plant Cell DOI: 10.1101/2020.10.02.324327 Protocol: 10x Genomics Tissues: Lateral root No. Cells: 6,658 |
| E-MTAB-9174 | Single-nucleus RNA sequencing of plant tissues using a nanowell-based system Authors: Sunaga-Franze et al., Publication Date: 2020.11.16 Journal: bioRxiv DOI: 10.1101/2020.11.14.382812 Protocol: Nanowell-based approach Tissues: Root; Leaf; Flower; Silique; Stem No. Cells: 3,727 |
| PRJNA664874 | FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants Authors: Long et al., Publication Date: 2021.02.19 Journal: Genome Biology DOI: 10.1101/2020.11.25.397919 Protocol: 10x Genomics Tissues: Root/embryo No. Cells: |
| PRJNA716169 | Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution Authors: Kao et al., Publication Date: 2021.03.26 Journal: bioRxiv DOI: 10.1101/2021.03.26.437151 Protocol: Smart-seq2 Tissues: Embryo No. Cells: 534 |
| PRJNA730707 | A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data Authors: Neumann et al., Publication Date: 2021.07.01 Journal: Nature communications DOI: 10.1101/2021.06.30.450319 Protocol: 10x Genomics Tissues: Floral meristem No. Cells: 7716 |
| PRJNA507252 | Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells Authors: Ryu et al., Publication Date: 2019.04.09 Journal: Plant Physiology DOI: 10.1104/pp.18.01482 Protocol: 10x Genomics Tissues: Root No. Cells: >10,000 |
| PRJNA497883 | Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana Authors: Jean-Baptiste et al., Publication Date: 2019.05.31 Journal: The Plant Cell DOI: 10.1105/tpc.18.00785 Protocol: 10x Genomics Tissues: Root No. Cells: 3,121 |
| PRJNA648028 | Stochastic gene expression drives mesophyll protoplast regeneration Authors: Xu et al., Publication Date: 2021.08.11 Journal: Science Advance DOI: 10.1126/sciadv.abg8466 Protocol: 10x Genomics Tissues: Leaf No. Cells: 6,683 |
| PRJNA594539 | Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions Authors: Wendrich et al., Publication Date: 2020.09.17 Journal: Science DOI: 10.1126/science.aay4970 Protocol: 10x Genomics Tissues: Root No. Cells: 15,918 |
| PRJNA490038 | Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes Authors: Song et al., Publication Date: 2020.06.22 Journal: Genome Biology DOI: 10.1186/s13059-020-02094-0 Protocol: Smart-seq2 Tissues: Female gametic cells No. Cells: / |
| PRJNA754157 | A root phloem pole cell atlas reveals common transcriptional states in protophloem-adjacent cells Authors: Otero et al., Publication Date: 2022.08.04 Journal: Nature Plant DOI: 10.17863/CAM.74836 Protocol: 10x Genomics Tissues: Root No. Cells: 10204 |
| CNP0002618 | The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves Authors: Xia et al., Publication Date: 2022.05.23 Journal: Developmental Cell DOI: doi.org/10.1016/j.devcel.2022.04.011 Protocol: Stereo-seq Tissues: Leaf No. Cells: / |
Oryza sativa
Totally 4 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| CRA004082 | Single-cell transcriptome atlas of the leaf and root of rice seedlings Authors: Wang et al., Publication Date: 2021.06.18 Journal: Journal of Genetics and Genomics DOI: 10.1016/j.jgg.2021.06.001 Protocol: 10x Genomics Tissues: Leaf, Root No. Cells: 237,431 |
| PRJNA609092 | Transcriptional Landscape of Rice Roots at the Single Cell Resolution Authors: Liu et al., Publication Date: 2020.12.16 Journal: Molecular Plant DOI: 10.1016/j.molp.2020.12.014 Protocol: 10x Genomics Tissues: Root No. Cells: 23,532 |
| PRJNA706435 | Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root Authors: Zhang et al., Publication Date: 2021.04.06 Journal: Nature Communication DOI: 10.1038/s41467-021-22 Protocol: 10x Genomics(scRNA+scATAC) Tissues: Root No. Cells: 27,469 |
| PRJNA767589 | A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems Authors: Zong et al., Publication Date: 2022.02.04 Journal: New Phytologist DOI: 10.1111/nph.18008 Protocol: BD Rhapsody system Tissues: Inflorescence No. Cells: 37,571 |
Solanum lycopersicum
Totally 2 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA661700 | Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex Authors: Tian et al., Publication Date: 2020.12.14 Journal: bioRxiv DOI: 10.1101/2020.09.20.305029 Protocol: 10x Genomics Tissues: Shoot apex No. Cells: 13,377 |
| PRJNA667489 | A conserved superlocus regulates above-and belowground root initiation Authors: Omary et al., Publication Date: 2020.11.16 Journal: Science DOI: 10.1101/2020.11.11.377937 Protocol: mc-SCRB Tissues: Shoot borne root No. Cells: 960 |
Zea mays
Totally 10 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA648930 | A cis-regulatory atlas in maize at single-cell resolution Authors: Marand et al., Publication Date: 2021.05.27 Journal: Cell DOI: 10.1016/j.cell.2021.04.014 Protocol: ATAC(10X Genomics) Tissues: Seedling No. Cells: 56,575 |
| PRJNA759548 | Single-cell RNA sequencing reveals the landscape of maize root tips and assists in identification of cell type-specific nitrate-response genes Authors: Li et al., Publication Date: 2022.03.09 Journal: The Crop Journal DOI: 10.1016/j.cj.2022.02.004 Protocol: 10x Genomics Tissues: Root No. Cells: 7,000 |
| PRJNA646989 & PRJNA646996 & PRJNA647001 | Single-Cell RNA Sequencing of Developing Ears Facilitates Functional Analysis and Trait Candidate Gene Discovery Authors: Xu et al., Publication Date: 2021.01.04 Journal: Developmetnal Cell DOI: 10.1016/j.devcel.2020.12.015 Protocol: 10x Genomics Tissues: Ears No. Cells: 12,525 |
| PRJNA662627 | Evidence for Phloem Loading via the Abaxial Bundle Sheath Cells in Maize Leaves Authors: Bezrutczyk et al., Publication Date: 2021.01.14 Journal: The Plant Cell DOI: 10.1093/plcell/koaa055 Protocol: 10x Genomics Tissues: Leaf No. Cells: 3,763 |
| PRJNA740934 | The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata Authors: Sun et al., Publication Date: 2022.02.15 Journal: The Plant Cell DOI: 10.1093/plcell/koac047 Protocol: 10x Genomics Tissues: Leaf No. Cells: 33098 |
| PRJNA637882 | Plant stem cell organization and differentiation at single-cell resolution Authors: Satterlee et al., Publication Date: 2020.08.25 Journal: PNAS DOI: 10.1101/2020.08.25.267427 Protocol: 10x Genomics & CEL-seq2 Tissues: Shoot apical No. Cells: 13,377 |
| PRJNA760550 | FX-Cell: Quantitative cell release from fixed plant tissues for single-cell genomics Authors: Marchant et al., Publication Date: 2021.10.11 Journal: bioRxiv DOI: 10.1101/2021.10.11.463960 Protocol: CEL-Seq2 Tissues: Anther No. Cells: / |
| PRJNA495390 | Defining the developmental program leading to meiosis in maize Authors: Nelms et al., Publication Date: 2019.04.05 Journal: Science DOI: 10.1126/science.aav6428 Protocol: CEL-seq2 Tissues: Anther No. Cells: 213 |
| PRJNA454730 | Ground tissue circuitry regulates organ complexity in maize and Setaria Authors: Ortiz-Ramirez et al., Publication Date: 2021.12.03 Journal: Science DOI: 10.1126/science.abj2327 Protocol: 10x Genomics Tissues: Root No. Cells: 14,755 |
| PRJNA576240 | Single-Cell Transcriptome and Network Analyses Unveil Key Transcription Factors Regulating Mesophyll Cell Development in Maize Authors: Tao et al., Publication Date: 2022.02.20 Journal: Genes DOI: 10.3390/genes13020374 Protocol: 10x Genomics Tissues: Leaf No. Cells: 14,656 |
Fragaria vesca
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| CRA004848 | Development of a single-cell atlas for woodland strawberry (Fragaria vesca) leaves during early Botrytis cinerea infection using single cell RNA-seq Authors: Bai et al., Publication Date: 2022.01.19 Journal: Horticulture Research DOI: 10.1093/hr/uhab055 Protocol: 10x Genomics Tissues: Leaf No. Cells: 15,039 |
Populus
Totally 3 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA787915 | Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus Authors: Conde et al., Publication Date: 2021.12.28 Journal: Development DOI: 10.1101/2021.12.28.474348 Protocol: 10x Genomics Tissues: Vegetative shoot apex No. Cells: / |
| PRJNA703312 | Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus Authors: Li et al., Publication Date: 2021.08.02 Journal: Journal of Integrative Plant Biology DOI: 10.1111/jipb.13159 Protocol: 10x Genomics Tissues: Shoot No. Cells: 9,798 |
| PRJCA005543 | Transcriptional landscape of highly lignified poplar stems at single-cell resolution Authors: Chen et al., Publication Date: 2021.11.22 Journal: Genome Biology DOI: 10.1186/s13059-021-02537-2 Protocol: 10x Genomics Tissues: Stem No. Cells: 3,626;3,170 |
Nicotiana attenuata
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA796301 | Single-cell RNA-sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent Authors: Kang et al., Publication Date: 2021.06.28 Journal: New Phytologist DOI: 10.1101/2021.06.28.450226 Protocol: 10x Genomics Tissues: Corolla No. Cells: 3,756 |
Lemna minuta
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| SAMN19243672 | The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness Authors: Abramson et al., Publication Date: 2021.06.03 Journal: Plant Physiology DOI: 10.1101/2021.06.03.446947 Protocol: Smart-seq2 Tissues: Whole plant No. Cells: 269 |
Chlamydomonas reinhardtii
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA662042 | Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase Authors: Ma et al., Publication Date: 2021.02.02 Journal: The Plant Cell DOI: 10.1093/plcell/koab025 Protocol: 10x Genomics Tissues: Chlamydomonas reinhardtii No. Cells: 30,000 |
Brassica rapa
Totally 2 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJCA009630 | Single-cell transcriptome reveals differentiation between adaxial and abaxial mesophyll cells in Brassica rapa Authors: Guo et al., Publication Date: 2022.09.23 Journal: Plant Biotechnology Journal DOI: 10.1111/pbi.13919 Protocol: 10x Genomics Tissues: Leaf No. Cells: 16055 |
| PRJCA013085 | Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage Authors: Sun et al., Publication Date: 2022.12.19 Journal: Genome Biology DOI: 10.1186/s13059-022-02834-4 Protocol: 10x Genomics Tissues: Shoot apex No. Cells: 30000 |
Manihot esculenta
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA895163 | Single-cell transcriptome sequencing atlas of cassava tuberous root. Authors: Song et al., Publication Date: 2023.1.4 Journal: Frontiers in plant science DOI: 3389.2022/fpls.1053669 Protocol: 10x Genomics Tissues: Root No. Cells: / |
Medicago truncatula
Totally 2 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJCA012129 | Differentiation trajectories and biofunctions of symbiotic and un-symbiotic fate cells in root nodules of Medicago truncatula Authors: Ye et al., Publication Date: 2022.10.23 Journal: Molecular Plant DOI: 10.1016/j.molp.2022.10.019 Protocol: 10x Genomics Tissues: Root No. Cells: 9756 |
| PRJNA868047 | Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume Authors: Cervantes-Pérez et al., Publication Date: 2022.10.27 Journal: Molecular Plant DOI: 10.1016/j.molp.2022.10.021 Protocol: 10x Genomics Tissues: Root No. Cells: 28375 |
Nepeta tenuifolia
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA743551 | Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation in glandular trichomes Authors: Zhou et al., Publication Date: 2022.10.19 Journal: Frontiers in Plant Science DOI: 10.3389/fpls.2022.988594 Protocol: 10x Genomics Tissues: Leaf No. Cells: 33254 |
Gossypium hirsutum
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA600131 | Single-cell RNA-seq reveals fate determination control of an individual fiber cell initiation in cotton (Gossypium hirsutum) Authors: Qin et al., Publication Date: 2022.08.29 Journal: Plant Biotechnology Journal DOI: 10.1111/pbi.13918 Protocol: 10x Genomics Tissues: Ovule No. Cells: 14535 |
Glycine max
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJCA009893 | Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment Authors: Liu et al., Publication Date: 2023.04.13 Journal: Nature Plants(Brief Communication) DOI: 10.1038/s41477-023-01387-Z Protocol: Stereo-seq Tissues: nodules No. Cells: / |
Phalaenopsis aphrodite
Totally 1 papers
| Dataset ID | Detailed infomation of datasets |
|---|---|
| PRJNA813957 | A spatiotemporal atlas of organogenesis in the development of orchid flowers Authors: Liu et al., Publication Date: 2022.09.23 Journal: Nucleic Acids Res DOI: 10.1093/nar/gkac773 Protocol: 10x Genomics Visium Tissues: Flower No. Cells: / |