References

Public datasets used by PlantscRNAdb

Arabidopsis thaliana

Totally 20 papers

Dataset IDDetailed infomation of datasets
Not available Transcriptomics of Arabidopsis sperm cells at single-cell resolution
Authors: "Misra et al.," Publication Date: 2019.01.24 Journal: Plant Reproduction DOI: 10.1007/s00497-018-00355-4
Protocol: Smart-seq2 Tissues: sperm cells No. Cells: 80
GSE74488 Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions
Authors: "Efroni et al.," Publication Date: 2016.06.16 Journal: Cell DOI: 10.1016/j.cell.2016.04.046
Protocol: CEL-seq2 Tissues: root No. Cells: /
GSE122687 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: 10x Genomics Tissues: root No. Cells: ">12,000"
GSE114615 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
GSE123818 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"
PRJNA323955 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"
GSE155304 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: 10548
GSE161482 Unique and distinct identities and functions 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 vasculature No. Cells: "5,230"
GSE152766 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: bioRxiv DOI: 10.1101/2020.06.29.178863
Protocol: 10x Genomics Tissues: root No. Cells: "110,000"
pending Single nucleus analysis of Arabidopsis seeds reveals new cell types and imprinting dynamics
Authors: "Picard et al.," Publication Date: 2020.08.25 Journal: bioRxiv DOI: 10.1101/2020.08.25.267476
Protocol: / Tissues: seed No. Cells: "1,437"
pending 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: bioRxiv DOI: 10.1101/2020.09.08.288498
Protocol: 10x Genomics & Smart-seq2 Tissues: whole aerial tissue or first true leaves No. Cells: "18,000"
pending A single cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana
Authors: "Gala et al.," Publication Date: 2020.10.02 Journal: bioRxiv DOI: 10.1101/2020.10.02.324327
Protocol: 10x Genomics Tissues: lateral root No. Cells: "6,658"
E-MTAB-9174 Single-nuclei RNA-sequencing of plants
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;seed;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: 1762
GSE123013 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"
GSE121619 Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana
Authors: "Jean-Baptiste et al.," Publication Date: 2019.05. Journal: The Plant Cell DOI: 10.1105/tpc.18.00785
Protocol: 10x Genomics Tissues: root No. Cells: "3,121"
GSE141730 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"
GSE46226 Quantification of cell identity from single-cell gene expression profiles
Authors: "Efroni et al.," Publication Date: 2015.01.22 Journal: Genome Biology DOI: 10.1186/s13059-015-0580-x
Protocol: / Tissues: root No. Cells: 31
SRP160651 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: / Tissues: female gametic cells No. Cells:

Oryza sativa

Totally 2 papers

Dataset IDDetailed infomation of datasets
GSE146035 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"
pending Single-cell transcriptome analyses recapitulate the cellular and developmental responses to abiotic stresses in rice
Authors: "Wang et al.," Publication Date: 2020.01.30 Journal: bioRxiv DOI: 10.1101/2020.01.30.926329
Protocol: 10x Genomics Tissues: the aerial part of rice seedlings No. Cells: "4,580"

Solanum lycopersicum

Totally 1 papers

Dataset IDDetailed infomation of datasets
SAMN16069893 Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex
Authors: "Tian et al.," Publication Date: 2020.09.20 Journal: bioRxiv DOI: 10.1101/2020.09.20.305029
Protocol: 10x Genomics Tissues: shoot apex No. Cells: "13,377"

Zea mays

Totally 4 papers

Dataset IDDetailed infomation of datasets
PRJNA646989 & PRJNA646996 & PRJNA647001 Single-Cell RNA Sequencing of Developing Ears Facilitates Functional Analysis and Trait Candidate Gene Discovery in Maize
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: 12525
GSE157759Evidence 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: 3763
PRJNA637882 Plant stem cell organization and differentiation at single-cell resolution
Authors: "Satterlee et al.," Publication Date: 2020.08.25 Journal: bioRxiv DOI: 10.1101/2020.08.25.267427
Protocol: 10x Genomics & CEL-seq2 Tissues: shoot apical meristems No. Cells: /
GSE121039 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