Use our table below to examine 186 single cell plant papers we are curating. 72 of these have links to data viewers! Here are some stats for these papers:
| Title | Authors | Author is PCA Member* | Citation | DOI | Published Cell Number | Repository Record | Link to COPO Manifest | Link to Data Viewer(s) | Species |
|---|---|---|---|---|---|---|---|---|---|
| The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness | Abramson BW, Novotny M, Hartwick NT, Colt K, Aevermann BD, Scheuermann RH, Michael TP | Plant Physiol. 2022 Feb 4;188(2):879-897. doi: 10.1093/plphys/kiab564. | 10.1093/plphys/kiab564 | 269 | SAMN19243672 | Lemna minuta | |||
| Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles | Apelt F, Mavrothalassiti E, Gupta S, Machin F, Olas JJ, Annunziata MG, Schindelasch D, Kragler F | Plant Physiol. 2022 Feb 4;188(2):861-878. doi: 10.1093/plphys/kiab537. | 10.1093/plphys/kiab537 | 69131 | PRJNA742744 | Arabidopsis thaliana | |||
| Development of a single-cell atlas for woodland strawberry (Fragaria vesca) leaves during early Botrytis cinerea infection using single cell RNA-seq | Bai Y, Liu H, Lyu H, Su L, Xiong J, Cheng ZM | Hortic Res. 2022 Jan 19;9:uhab055. doi: 10.1093/hr/uhab055. Online ahead of print. | 10.1093/hr/uhab055 | 50327 | CRA004848 | scPlantDB | Fragaria vesca | ||
| Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves | Bezrutczyk M, Zöllner NR, Kruse CPS, Hartwig T, Lautwein T, Köhrer K, Frommer WB, Kim JY | Plant Cell. 2021 May 5;33(3):531-547. doi: 10.1093/plcell/koaa055. | 10.1093/plcell/koaa055 | 10901 | SRP281914 | scPlantDB, SCEA | Zea mays | ||
| A common regulatory switch controls a suite of C4 traits in multiple cell types | Camo-Escobar D, Alcalá-Gutiérrez C, Palafox-Figueroa E, Guillotin B, Hernández-Coronado M, Coyac-Rodríguez JL, Cerbantez-Bueno VE, Vélez-Ramírez A, de Folter S, Birnbaum K*, Ortiz-Ramírez C | Yes | bioRxiv [Preprint]. 2024 Jan 9:2023.12.21.572850. doi: 10.1101/2023.12.21.572850. | 10.1101/2023.12.21.572850 | n/a | GSE249836 | Setaria viridis | ||
| A suberized exodermis is required for tomato drought tolerance | Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, Nirmal N, Suresh K, Ursache R, Mason GA, Gouran M, West DA, Borowsky AT, Shackel KA, Sinha N, Bailey-Serres J*, Geldner N, Li S*, Franke RB, Brady SM* | Yes | Nat Plants. 2024 Jan;10(1):118-130. doi: 10.1038/s41477-023-01567-x. Epub 2024 Jan 2. | 10.1038/s41477-023-01567-x | 22207 | GSE212405 | Solanum lycopersicum | ||
| Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress | Cao J, Ye C, Hao G, Dabney-Smith C, Hunt AG, Li QQ | Front Plant Sci. 2019 May 10;10:589. doi: 10.3389/fpls.2019.00589. eCollection 2019. | 10.3389/fpls.2019.00589 | n/a | PRJNA477396 | Arabidopsis thaliana | |||
| Single-cell RNA sequencing profiles reveal cell type-specific transcriptional regulation networks conditioning fungal invasion in maize roots | Cao Y, Ma J, Han S, Hou M, Wei X, Zhang X, Zhang ZJ, Sun S, Ku L, Tang J, Dong Z, Zhu Z, Wang X, Zhou X, Zhang L, Li X, Long Y, Wan X, Duan C | Plant Biotechnol J. 2023 Sep;21(9):1839-1859. doi: 10.1111/pbi.14097. Epub 2023 Jun 22. | 10.1111/pbi.14097 | 29217 | PRJNA865791 | Zea mays | |||
| Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume | Cervantes-Pérez SA, Thibivilliers S, Laffont C, Farmer AD*, Frugier F, Libault M* | Yes | Mol Plant. 2022 Dec 5;15(12):1868-1888. doi: 10.1016/j.molp.2022.10.021. Epub 2022 Nov 1. | 10.1016/j.molp.2022.10.021 | 28375 | SRP390780 | scPlantDB | Medicago truncatula | |
| Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process | Cervantes-Pérez SA, Zogli P, Amini S*, Thibivilliers S, Tennant S, Hossain MS, Xu H, Meyer I, Nooka A, Ma P, Yao Q*, Naldrett MJ, Farmer A*, Martin O, Bhattacharya S, Kläver J, Libault M* | Yes | Plant Commun. 2024 Aug 12;5(8):100984. doi: 10.1016/j.xplc.2024.100984. Epub 2024 Jun 6. | 10.1016/j.xplc.2024.100984 | 21521 | PRJNA938968 | Glycine max | ||
| Single-cell transcriptome sequencing revealing the difference in photosynthesis and carbohydrate metabolism between epidermal cells and non-epidermal cells of Gracilariopsis lemaneiformis (Rhodophyta) | Chen H, Hu Y, Li P, Feng X, Jiang M, Sui Z | Front Plant Sci. 2022 Nov 17;13:968158. doi: 10.3389/fpls.2022.968158. eCollection 2022. | 10.3389/fpls.2022.968158 | n/a | PRJNA752461 | Gracilariopsis lemaneiformis | |||
| Single-cell transcriptomic analysis of pea shoot development and cell-type-specific responses to boron deficiency | Chen X, Ru Y, Takahashi H, Nakazono M, Shabala S, Smith SM, Yu M | Plant J. 2024 Jan;117(1):302-322. doi: 10.1111/tpj.16487. Epub 2023 Oct 5. | 10.1111/tpj.16487 | 23705 | PRJNA983513 | Pisum sativum | |||
| Identification of maize genes conditioning the early systemic infection of sugarcane mosaic virus by single-cell transcriptomics | Chen X, Yao R, Hua X, Du K, Liu B, Yuan Y, Wang P, Yan Q, Dong L, Groen SC, Jiang S, Zhou T | Plant Commun. 2025 Mar 4:101297. doi: 10.1016/j.xplc.2025.101297. Online ahead of print. | 10.1016/j.xplc.2025.101297 | n/a | CRA014755 | Zea mays | |||
| Transcriptional landscape of highly lignified poplar stems at single-cell resolution | Chen Y, Tong S, Jiang Y, Ai F, Feng Y, Zhang J, Gong J, Qin J, Zhang Y, Zhu Y, Liu J, Ma T | Genome Biol. 2021 Nov 22;22(1):319. doi: 10.1186/s13059-021-02537-2. | 10.1186/s13059-021-02537-2 | 6796 | CRA004476 | scPlantDB | Populus alba var. pyramidalis | ||
| Single-cell RNA sequencing reveals dynamics of gene expression for 2D elongation and 3D growth in Physcomitrium patens | Chen Z, Wang W, Zhou S, Ding L, Xu Z, Sun X, Huo H, Liu L | Cell Rep. 2024 Aug 27;43(8):114524. doi: 10.1016/j.celrep.2024.114524. Epub 2024 Jul 23. | 10.1016/j.celrep.2024.114524 | 11489 | CRA013145 | Physcomitrium patens | |||
| Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo (Phyllostachys edulis) | Cheng Z, Mu C, Li X, Cheng W, Cai M, Wu C, Jiang J, Fang H, Bai Y, Zheng H, Geng R, Xu J, Xie Y, Dou Y, Li J, Mu S, Gao J | Hortic Res. 2023 Jun 9;10(8):uhad122. doi: 10.1093/hr/uhad122. eCollection 2023 Aug. | 10.1093/hr/uhad122 | 15324 | GSE229126 | Phyllostachy sedulis | |||
| Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus | Conde D, Triozzi PM, Pereira WJ, Schmidt HW, Balmant KM, Knaack SA, Redondo-López A, Roy S, Dervinis C, Kirst M | Development. 2022 Nov 1;149(21):dev200632. doi: 10.1242/dev.200632. Epub 2022 Oct 17. | 10.1242/dev.200632 | 8324 | GSE190649 | Populus tremula×alba | |||
| Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit | Cui Y, Su Y, Bian J, Han X, Guo H, Yang Z, Chen Y, Li L, Li T, Deng XW, Liu X | Plant Commun. 2024 Aug 12;5(8):100979. doi: 10.1016/j.xplc.2024.100979. Epub 2024 May 24. | 10.1016/j.xplc.2024.100979 | 49896 | PRJNA1068272 | Liu Lab Viewer | Arachis hypogaea | ||
| Single-cell transcriptomic analysis of flowering regulation and vernalization in Chinese cabbage shoot apex | Dai Y, Zhang S, Guan J, Wang S, Zhang H, Li G, Sun R, Li F, Zhang S | Hortic Res. 2024 Jul 30;11(10):uhae214. doi: 10.1093/hr/uhae214. eCollection 2024 Oct. | 10.1093/hr/uhae214 | n/a | CRA014199 | Brassica rapa L. ssp. pekinensis | |||
| Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq | Delannoy E, Batardiere B, Pateyron S, Soubigou-Taconnat L, Chiquet J, Colcombet J, Lang J | Plant Commun. 2023 Sep 11;4(5):100676. doi: 10.1016/j.xplc.2023.100676. Epub 2023 Aug 28. | 10.1016/j.xplc.2023.100676 | 11206 | PRJNA995336 | Arabidopsis thaliana | |||
| ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L | Deng Q, Du P, Gangurde SS, Hong Y, Xiao Y, Hu D, Li H, Lu Q, Li S, Liu H, Wang R, Huang L, Wang W, Garg V, Liang X, Varshney RK, Chen X, Liu H | Plant Biotechnol J. 2024 Jul;22(7):1848-1866. doi: 10.1111/pbi.14306. Epub 2024 Feb 23. | 10.1111/pbi.14306 | n/a | PRJCA010983, PRJCA015968 | Arachis hypogaea | |||
| Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing | Denyer T, Ma X, Klesen S, Scacchi E, Nieselt K, Timmermans MCP | Dev Cell. 2019 Mar 25;48(6):840-852.e5. doi: 10.1016/j.devcel.2019.02.022. | 10.1016/j.devcel.2019.02.022 | 4727 | SRP173393 | scPlantDB | Arabidopsis thaliana | ||
| Single-cell RNA landscape of the special fiber initiation process in Bombax ceiba | Ding Y, Gao W, Qin Y, Li X, Zhang Z, Lai W, Yang Y, Guo K, Li P, Zhou S, Hu H | Plant Commun. 2023 Sep 11;4(5):100554. doi: 10.1016/j.xplc.2023.100554. Epub 2023 Feb 10. | 10.1016/j.xplc.2023.100554 | 15567 | CRA009614 | scPlantDB | Bombax ceiba | ||
| The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution | Dorrity MW, Alexandre CM, Hamm MO, Vigil AL, Fields S, Queitsch C, Cuperus JT | Nat Commun. 2021 Jun 7;12(1):3334. doi: 10.1038/s41467-021-23675-y. | 10.1038/s41467-021-23675-y | 5283 | GSE173834 | Arabidopsis thaliana | |||
| Single-Cell RNA Sequencing Reveals the Developmental Landscape of Wheat Roots | Du Z, Zhang B, Weng H, Gao L | Plant Cell Environ. 2025 Jan 6. doi: 10.1111/pce.15321. Online ahead of print. | 10.1111/pce.15321 | 13063 | GSE222422 | Triticum aestivum | |||
| Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level | Farmer A*, Thibivilliers S, Ryu KH, Schiefelbein J, Libault M* | Yes | Mol Plant. 2021 Mar 1;14(3):372-383. doi: 10.1016/j.molp.2021.01.001. Epub 2021 Jan 7. | 10.1016/j.molp.2021.01.001 | 10758 | SRP273996 | scPlantDB | Arabidopsis thaliana | |
| Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips | Feng D, Liang Z, Wang Y, Yao J, Yuan Z, Hu G, Qu R, Xie S, Li D, Yang L, Zhao X, Ma Y, Lohmann JU, Gu X | BMC Biol. 2022 Dec 8;20(1):274. doi: 10.1186/s12915-022-01473-2. | 10.1186/s12915-022-01473-2 | 25312 | GSE214132 | Oryza sativa | |||
| Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development | Feng H, Fan W, Liu M, Huang J, Li B, Sang Q, Song B | BMC Genomics. 2025 Jan 3;26(1):3. doi: 10.1186/s12864-024-11186-1. | 10.1186/s12864-024-11186-1 | 21861 | PRJCA023192 | Zea mays, Sorghum bicolor | |||
| Single-cell transcriptome analyses reveal cellular and molecular responses to low nitrogen in burley tobacco leaves | Feng Y, Zhao Y, Ma Y, Liu D, Shi H | Physiol Plant. 2023 Nov-Dec;175(6):e14118. doi: 10.1111/ppl.14118. | 10.1111/ppl.14118 | 21351 | CRA012100 | Nicotiana tabacum | |||
| Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus | Frank M , Fechete LI, Tedeschi F, Nadzieja M, Nørgaard MMM, Montiel J, Andersen KR, Schierup MH, Reid D, Andersen SU | Nat Commun. 2023 Nov 7;14(1):7171. doi: 10.1038/s41467-023-42911-1. | 10.1038/s41467-023-42911-1 | 67258 | PRJEB57790 | Single Cell Lotus japonicus viewer | Lotus japonicus | ||
| A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana | Gala HP, Lanctot A, Jean-Baptiste K, Guiziou S, Chu JC, Zemke JE, George W, Queitsch C, Cuperus JT, Nemhauser JL | Plant Cell. 2021 Aug 13;33(7):2197-2220. doi: 10.1093/plcell/koab101. | 10.1093/plcell/koab101 | 9090 | SRP285817 | scPlantDB, SCEA | Arabidopsis thaliana | ||
| Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos | Ge X, Yu X, Liu Z, Yuan J, Qin A, Wang Y, Chen Y, Qin W, Liu Y, Liu X, Zhou Y, Wang P, Yang J, Liu H, Zhao Z, Hu M, Zhang Y, Sun S, Herrera-Estrella L, Tran LP, Sun X, Li F | Nat Commun. 2025 Jan 20;16(1):859. doi: 10.1038/s41467-025-55870-6. | 10.1038/s41467-025-55870-6 | n/a | PRJNA800600 | scPlantDB | Gossypium spp. | ||
| Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression | Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ, Locke JC | Elife. 2018 Apr 26;7:e31700. doi: 10.7554/eLife.31700. | 10.7554/eLife.31700 | n/a | n/a | Arabidopsis thaliana | |||
| A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root | Graeff M, Rana S, Wendrich JR, Dorier J, Eekhout T, Aliaga Fandino AC, Guex N, Bassel GW, De Rybel B, Hardtke CS | Mol Plant. 2021 Dec 6;14(12):1985-1999. doi: 10.1016/j.molp.2021.07.021. Epub 2021 Aug 4. | 10.1016/j.molp.2021.07.021 | 12491 | SRP330542 | scPlantDB | Arabidopsis thaliana | ||
| A pan-grass transcriptome reveals patterns of cellular divergence in crops | Guillotin B*, Rahni R*, Passalacqua M*, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D*, Groen SC, Gillis J, Birnbaum KD* | Yes | Nature. 2023 May;617(7962):785-791. doi: 10.1038/s41586-023-06053-0. Epub 2023 May 10. | 10.1038/s41586-023-06053-0 | 69215 | GSE225118 | Arabidopsis thaliana, Zea mays, Sorghum bicolor, Setaria viridis | ||
| Cell Fate Determination of the Potato Shoot Apex and Stolon Tips Revealed by Single-Cell Transcriptome Analysis | Guo C, Huang Z, Luo S, Wang X, Li J, Yu G, Wang Y, Wang X | Plant Cell Environ. 2025 Mar 17. doi: 10.1111/pce.15459. Online ahead of print. | 10.1111/pce.15459 | n/a | PRJCA020216 | Solanum tuberosum | |||
| Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration | Guo H, Zhang L, Guo H, Cui X, Fan Y, Li T, Qi X, Yan T, Chen A, Shi F, Zeng F | Plant Physiol. 2024 May 31;195(2):1414-1431. doi: 10.1093/plphys/kiae107. | 10.1093/plphys/kiae107 | n/a | n/a | Gossypium hirsutum | |||
| Single-cell transcriptome reveals differentiation between adaxial and abaxial mesophyll cells in Brassica rapa | Guo X, Liang J, Lin R, Zhang L, Zhang Z, Wu J, Wang X | Plant Biotechnol J. 2022 Dec;20(12):2233-2235. doi: 10.1111/pbi.13919. Epub 2022 Sep 16. | 10.1111/pbi.13919 | 30590 | CRA006988 | scPlantDB | Brassica rapa | ||
| An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation | Guo X, Wang Y, Zhao C, Tan C, Yan W, Xiang S, Zhang D, Zhang H, Zhang M, Yang L, Yan M, Xie P, Wang Y, Li L, Fang D, Guang X, Shao W, Wang F, Wang H, Sahu SK, Liu M, Wei T, Peng Y, Qiu Y, Peng T, Zhang Y, Ni X, Xu Z, Lu H, Li Z, Yang H, Wang E, Lisby M, Liu H, Guo H, Xu X | Cell. 2025 Apr 10:S0092-8674(25)00297-1. doi: 10.1016/j.cell.2025.03.024. Online ahead of print. | 10.1016/j.cell.2025.03.024 | 913769 | CNP0002614 | Arabidopsis thaliana | |||
| Single-cell RNA sequencing reveals a high-resolution cell atlas of petals in Prunus mume at different flowering development stages | Guo Y, Chen X, Li J, Wang Q, Zhang S, Liu N, Zhang Y, Zhang T | Hortic Res. 2024 Jul 10;11(9):uhae189. doi: 10.1093/hr/uhae189. eCollection 2024 Sep. | 10.1093/hr/uhae189 | 16948 | n/a | Prunus mume | |||
| Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings | Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H, Deng XW | Nat Plants. 2023 Dec;9(12):2095-2109. doi: 10.1038/s41477-023-01544-4. Epub 2023 Oct 30. | 10.1038/s41477-023-01544-4 | 98649 | PRJCA016521 | Arabidopsis thaliana | |||
| High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana | Hou Z, Liu Y, Zhang M, Zhao L, Jin X, Liu L, Su Z, Cai H, Qin Y | Commun Biol. 2021 Oct 1;4(1):1149. doi: 10.1038/s42003-021-02676-z. | 10.1038/s42003-021-02676-z | 16872 | PRJEB47244 | Arabidopsis thaliana | |||
| Evolution of a SHOOTMERISTEMLESS transcription factor binding site promotes fruit shape determination | Hu ZC, Majda M, Sun HR, Zhang Y, Ding YN, Yuan Q, Su TB, Lü TF, Gao F, Xu GX, Smith RS, Østergaard L, Dong Y | Nat Plants. 2025 Jan;11(1):23-35. doi: 10.1038/s41477-024-01854-1. Epub 2024 Dec 12. | 10.1038/s41477-024-01854-1 | 40629 | PRJNA1067523 | Capsella rubella | |||
| Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen | Ichino L, Picard CL, Yun J, Chotai M, Wang S, Lin EK, Papareddy RK, Xue Y, Jacobsen SE | Cell Rep. 2022 Nov 22;41(8):111699. doi: 10.1016/j.celrep.2022.111699. | 10.1016/j.celrep.2022.111699 | 86001 | SRP374045 | scPlantDB | Arabidopsis thaliana | ||
| Stress Recovery Triggers Rapid Transcriptional Reprogramming and Activation of Immunity in Plants | Illouz-Eliaz N*, Yu J, Swift J, Lande K, Jow B, Tuang ZK, Lee T, Yaaran A, Castanon RG, Nery JR, Nobori T*, Zait Y, Burdman S, Ecker JR | Yes | NA | 10.1101/2023.02.27.530256 | 144494 | GSE220278 | BAR Viewer | Arabidopsis thaliana | |
| Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana | Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L, Bubb KL, Trapnell C, Fields S, Queitsch C*, Cuperus JT* | Yes | Plant Cell. 2019 May;31(5):993-1011. doi: 10.1105/tpc.18.00785. Epub 2019 Mar 28. | 10.1105/tpc.18.00785 | 7777 | SRP166333 | scPlantDB, SCEA | Arabidopsis thaliana | |
| Single-cell RNA-sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent | Kang M, Choi Y, Kim H, Kim SG | New Phytol. 2022 Apr;234(2):527-544. doi: 10.1111/nph.17992. Epub 2022 Feb 15. | 10.1111/nph.17992 | 3756 | SRP354482 | scPlantDB | Nicotiana attenuata | ||
| Gene expression variation in Arabidopsis embryos at single-nucleus resolution | Kao P, Schon MA, Mosiolek M, Enugutti B, Nodine MD | Development. 2021 Jul 1;148(13):dev199589. doi: 10.1242/dev.199589. Epub 2021 Jul 6. | 10.1242/dev.199589 | 744 | SRP311577 | scPlantDB | Arabidopsis thaliana | ||
| Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures | Ke Y, Podio M, Conner J, Ozias-Akins P | Sci Rep. 2021 May 10;11(1):9880. doi: 10.1038/s41598-021-89170-y. | 10.1038/s41598-021-89170-y | n/a | n/a | Cenchrus ciliaris | |||
| A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators | Ke Y, Pujol V, Staut J, Pollaris L, Seurinck R, Eekhout T*, Grones C, Saura-Sanchez M, Van Bel M, Vuylsteke M, Ariani A, Liseron-Monfils C, Vandepoele K, Saeys Y, De Rybel B | Yes | Cell Rep. 2025 Feb 25;44(2):115240. doi: 10.1016/j.celrep.2025.115240. Epub 2025 Feb 1. | 10.1016/j.celrep.2025.115240 | 7388 | GSE270342 | VIB Plant sc-Atlas | Triticum aestivum | |
| Cell type-specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division | Kim EJ, Zhang C, Guo B, Eekhout T, Houbaert A, Wendrich JR, Vandamme N, Tiwari M, Simon-Vezo C, Vanhoutte I, Saeys Y, Wang K, Zhu Y, De Rybel B, Russinova E | Proc Natl Acad Sci U S A. 2023 Sep 5;120(36):e2303758120. doi: 10.1073/pnas.2303758120. Epub 2023 Aug 28. | 10.1073/pnas.2303758120 | 25862 | GSE193451 | Arabidopsis thaliana | |||
| Distinct identities of leaf phloem cells revealed by single cell transcriptomics | Kim JY, Symeonidi E, Pang TY, Denyer T, Weidauer D, Bezrutczyk M, Miras M, Zöllner N, Hartwig T, Wudick MM, Lercher M, Chen LQ, Timmermans MCP, Frommer WB | Plant Cell. 2021 May 5;33(3):511-530. doi: 10.1093/plcell/koaa060. | 10.1093/plcell/koaa060 | 5230 | SRP292306 | scPlantDB, SCEA | Arabidopsis thaliana | ||
| Glutathione accelerates the cell cycle and cellular reprogramming in plant regeneration | Lee LR, Guillotin B*, Rahni R, Hutchison C, Desvoyes B, Gutierrez C, Birnbaum KD* | Yes | Dev Cell. 2025 Jan 3:S1534-5807(24)00758-5. doi: 10.1016/j.devcel.2024.12.019. Online ahead of print. | 10.1016/j.devcel.2024.12.019 | n/a | GSE269623 | Arabidopsis thaliana | ||
| A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis | Lee TA, Nobori T*, Illouz-Eliaz N*, Xu J, Jow B, Nery JR, Ecker JR | Yes | bioRxiv [Preprint]. 2023 Sep 2:2023.03.23.533992v2. doi: 10.1101/2023.03.23.533992 | 10.1101/2023.03.23.533992 | 432919 | GSE226097 | Ecker Lab Viewer | Arabidopsis thaliana | |
| Cell-type-aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus | Li C, Colinas M*, Wood JC, Vaillancourt B, Hamilton JP, Jones SL, Caputi L, O'Connor SE, Buell CR | Yes | New Phytol. 2025 Jan;245(1):347-362. doi: 10.1111/nph.20208. Epub 2024 Oct 25. | 10.1111/nph.20208 | 8803 | PRJNA1098712 | Catharanthus roseus | ||
| Single-cell multi-omics in the medicinal plant Catharanthus roseus | Li C, Wood JC, Vu AH, Hamilton JP, Rodriguez Lopez CE, Payne RME, Serna Guerrero DA, Gase K, Yamamoto K, Vaillancourt B, Caputi L, O'Connor SE, Robin Buell C | Nat Chem Biol. 2023 Aug;19(8):1031-1041. doi: 10.1038/s41589-023-01327-0. Epub 2023 May 15. | 10.1038/s41589-023-01327-0 | 19797 | PRJNA847226 | Catharanthus roseus | |||
| Full-length RNA sequencing and single-nucleus sequencing deciphers programmed cell death and developmental trajectories in laticiferous canals of Decaisnea insignis fruits | Li G, Zhao Q, Shi X, Li B, Yang L, Wang Y, Zhou Y | Front Plant Sci. 2024 Aug 13;15:1446561. doi: 10.3389/fpls.2024.1446561. eCollection 2024. | 10.3389/fpls.2024.1446561 | 22260 | CRA016989 | Decaisnea insignis | |||
| Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus | Li H, Dai X, Huang X, Xu M, Wang Q, Yan X, Sederoff RR, Li Q | J Integr Plant Biol. 2021 Nov;63(11):1906-1921. doi: 10.1111/jipb.13159. Epub 2021 Oct 4. | 10.1111/jipb.13159 | 9798 | SRP307440 | scPlantDB | Populus alba x Populus glandulosa | ||
| Transcriptional Landscape of Cotton Roots in Response to Salt Stress at Single-cell Resolution | Li P, Liu Q, Wei Y, Xing C, Xu Z, Ding F, Liu Y, Lu Q, Hu N, Wang T, Zhu X, Cheng S, Li Z, Zhao Z, Li Y, Han J, Cai X, Zhou Z, Wang K, Zhang B, Liu F, Jin S, Peng R | Plant Commun. 2023 Oct 27;5(2):100740. doi: 10.1016/j.xplc.2023.100740. Online ahead of print. | 10.1016/j.xplc.2023.100740 | 56281 | GSE226218 | Gossypium arboreum | |||
| Single-cell transcriptome profiling reveals the spatiotemporal distribution of triterpenoid saponin biosynthesis and transposable element activity in Gynostemma pentaphyllum shoot apexes and leaves | Li R, Du K, Zhang C, Shen X, Yun L, Wang S, Li Z, Sun Z, Wei J, Li Y, Guo B, Sun C | Front Plant Sci. 2024 May 8;15:1394587. doi: 10.3389/fpls.2024.1394587. eCollection 2024. | 10.3389/fpls.2024.1394587 | 54968 | PRJNA1064230 | Gynostemma pentaphyllum | |||
| Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees | Li R, Wang Z, Wang JW, Li L | Plant Commun. 2023 Sep 11;4(5):100665. doi: 10.1016/j.xplc.2023.100665. Epub 2023 Jul 24. | 10.1016/j.xplc.2023.100665 | 19185 | CRA010013 | Populus euramericana | |||
| Single-cell transcriptomic and cell-type-specific regulatory networks in Polima temperature-sensitive cytoplasmic male sterility of Brassica napus L | Li S, Zhang J, Chen C, Ali A, Wen J, Dai C, Ma C, Tu J, Shen J, Fu T, Yi B | BMC Plant Biol. 2024 Dec 19;24(1):1206. doi: 10.1186/s12870-024-05916-6. | 10.1186/s12870-024-05916-6 | 34297 | CRA016609 | Brassica napus | |||
| Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence | Li X, Li B, Gu S, Pang X, Mason P, Yuan J, Jia J, Sun J, Zhao C, Henry R | Nat Commun. 2024 Apr 10;15(1):3108. doi: 10.1038/s41467-024-47329-x. | 10.1038/s41467-024-47329-x | 15917 | PRJNA974579 | Hylocereus undatus | |||
| Single-cell RNA sequencing of shoot apex reveals the mechanism of cyclin regulating cell division via auxin signaling pathway in Populus alba | Liang JH, Wu ZQ, Zhang YX, Yang YB, Wang SY, Gai MY, Wang YW, Zhang XX, Xue J, Duan BH, Yang HL | Front Plant Sci. 2025 Mar 4;16:1555388. doi: 10.3389/fpls.2025.1555388. eCollection 2025. | 10.3389/fpls.2025.1555388 | 29011 | n/a | Populus alba | |||
| Single-cell transcriptomic analyses reveal cellular and molecular patterns of rubber tree response to early powdery mildew infection | Liang X, Ma Z, Ke Y, Wang J, Wang L, Qin B, Tang C, Liu M, Xian X, Yang Y, Wang M, Zhang Y | Plant Cell Environ. 2023 Jul;46(7):2222-2237. doi: 10.1111/pce.14585. Epub 2023 Mar 24. | 10.1111/pce.14585 | 48823 | CRA008733 | Hevea brasiliensis | |||
| Establishment of single-cell transcriptional states during seed germination | Liew LC, You Y, Auroux L, Oliva M, Peirats-Llobet M*, Ng S, Tamiru-Oli M, Berkowitz O, Hong UVT, Haslem A, Stuart T, Ritchie ME, Bassel GW*, Lister R, Whelan J, Gouil Q, Lewsey MG | Yes | Nat Plants. 2024 Sep;10(9):1418-1434. doi: 10.1038/s41477-024-01771-3. Epub 2024 Sep 10. | 10.1038/s41477-024-01771-3 | 12798 | E-MTAB-12532 | sc-Germination Atlas, SCEA | Arabidopsis thaliana | |
| Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells | Lin JL, Chen L, Wu WK, Guo XX, Yu CH, Xu M, Nie GB, Dun JL, Li Y, Xu B, Wang LJ, Chen XY, Gao W, Huang JQ | Mol Plant. 2023 Dec 4;16(12):1990-2003. doi: 10.1016/j.molp.2023.10.008. Epub 2023 Oct 17. | 10.1016/j.molp.2023.10.008 | 22163 | GSE243419 | Gossypium hirsutum | |||
| Root-specific theanine metabolism and regulation at the single-cell level in tea plants (Camellia sinensis) | Lin S, Zhang Y, Zhang S, Wei Y, Han M, Deng Y, Guo J, Zhu B, Yang T, Xia E, Wan X, Lucas WJ, Zhang Z | Elife. 2024 Oct 14;13:RP95891. doi: 10.7554/eLife.95891. | 10.7554/eLife.95891 | 10435 | GSE267845 | Camellia sinensis | |||
| Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.) | Liu H, Hu D, Du P, Wang L, Liang X, Li H, Lu Q, Li H, Liu H, Chen X, Varshney RK, Hong Y | Plant Biotechnol J. 2021 Nov;19(11):2261-2276. doi: 10.1111/pbi.13656. Epub 2021 Jul 19. | 10.1111/pbi.13656 | 6815 | n/a | Arachis hypogaea | |||
| Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of quinoa salt bladders | Liu H, Liu Z, Zhou Y, Qin A, Li C, Liu Y, Gao P, Zhao Q, Song X, Li M, Kong L, Xie Y, Yan L, Guo E, Sun X | Stress Biol. 2024 Nov 13;4(1):47. doi: 10.1007/s44154-024-00189-3. | 10.1007/s44154-024-00189-3 | 15537 | CRA016880 | Chenopodium quinoa | |||
| Transcriptional landscape of rice roots at the single-cell resolution | Liu Q, Liang Z, Feng D, Jiang S, Wang Y, Du Z, Li R, Hu G, Zhang P, Ma Y, Lohmann JU, Gu X | Mol Plant. 2021 Mar 1;14(3):384-394. doi: 10.1016/j.molp.2020.12.014. Epub 2020 Dec 19. | 10.1016/j.molp.2020.12.014 | 23532 | SRP250946 | scPlantDB, SCEA_1, SCEA_2 | Oryza sativa | ||
| Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses | Liu W, Zhang Y, Fang X, Tran S, Zhai N, Yang Z, Guo F, Chen L, Yu J, Ison MS, Zhang T, Sun L, Bian H, Zhang Y, Yang L, Xu L | Plant Commun. 2022 Jul 11;3(4):100306. doi: 10.1016/j.xplc.2022.100306. Epub 2022 Feb 25. | 10.1016/j.xplc.2022.100306 | 7225 | SRP253497 | scPlantDB | Arabidopsis thaliana | ||
| Identification of the Regulators of Epidermis Development under Drought- and Salt-Stressed Conditions by Single-Cell RNA-Seq | Liu Z, Guo C, Wu R, Wang J, Zhou Y, Yu X, Zhang Y, Zhao Z, Liu H, Sun S, Hu M, Qin A, Liu Y, Yang J, Bawa G, Sun X | Int J Mol Sci. 2022 Mar 2;23(5):2759. doi: 10.3390/ijms23052759. | 10.3390/ijms23052759 | n/a | n/a | Arabidopsis thaliana | |||
| Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation | Liu Z, Kong X, Long Y, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J, Yan Z | Nat Plants. 2023 Apr;9(4):515-524. doi: 10.1038/s41477-023-01387-z. Epub 2023 Apr 13. | 10.1038/s41477-023-01387-z | 80136 | CRA007122 | scPlantDB | Glycine max | ||
| Identification of novel regulators required for early development of vein pattern in the cotyledons by single-cell RNA-sequencing | Liu Z, Wang J, Zhou Y, Zhang Y, Qin A, Yu X, Zhao Z, Wu R, Guo C, Bawa G, Rochaix JD, Sun | Plant J. 2022 Apr;110(1):7-22. doi: 10.1111/tpj.15719. Epub 2022 Mar 16. | 10.1111/tpj.15719 | 14117 | SRP247828_2 | scPlantDB | Arabidopsis thaliana | ||
| Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago | Liu Z, Yang J, Long Y, Zhang C, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J, Wang E | Nat Plants. 2023 Oct;9(10):1734-1748. doi: 10.1038/s41477-023-01524-8. Epub 2023 Sep 25. | 10.1038/s41477-023-01524-8 | 81421 | PRJCA011245 | Medicago truncatula | |||
| Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing | Liu Z, Zhou Y, Guo J, Li J, Tian Z, Zhu Z, Wang J, Wu R, Zhang B, Hu Y, Sun Y, Shangguan Y, Li W, Li T, Hu Y, Guo C, Rochaix JD, Miao Y, Sun X | Mol Plant. 2020 Aug 3;13(8):1178-1193. doi: 10.1016/j.molp.2020.06.010. Epub 2020 Jun 24. | 10.1016/j.molp.2020.06.010 | 46997 | SRP247828_1 | scPlantDB, SCEA | Arabidopsis thaliana | ||
| Single-cell transcriptome atlas identified novel regulators for pigment gland morphogenesis in cotton | Long L, Xu FC, Wang CH, Zhao XT, Yuan M, Song CP, Gao W | Plant Biotechnol J. 2023 Jun;21(6):1100-1102. doi: 10.1111/pbi.14035. Epub 2023 Mar 10. | 10.1111/pbi.14035 | n/a | n/a | Gossypium spp. | |||
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| Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf | Lopez-Anido CB, Vatén A, Smoot NK, Sharma N, Guo V, Gong Y, Anleu Gil MX, Weimer AK, Bergmann DC | Dev Cell. 2021 Apr 5;56(7):1043-1055.e4. doi: 10.1016/j.devcel.2021.03.014. | 10.1016/j.devcel.2021.03.014 | 18579 | SRP307169 | scPlantDB | Arabidopsis thaliana | ||
| Development of an inducible DNA barcoding system to understand lineage changes in Arabidopsis regeneration | Lu X, Zhang Q, Wang Z, Cheng X, Yan H, Cai S, Zhang H, Liu Q | Dev Cell. 2025 Jan 20;60(2):305-319.e5. doi: 10.1016/j.devcel.2024.10.023. Epub 2024 Nov 25. | 10.1016/j.devcel.2024.10.023 | n/a | n/a | Arabidopsis thaliana | |||
| The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth | Lyu M, Iida H, Eekhout T, Mäkelä M, Muranen S, Ye L, Vatén A, Wybouw B, Wang X, De Rybel B, Mähönen AP | Nat Plants. 2025 Mar 26. doi: 10.1038/s41477-025-01938-6. Online ahead of print. | 10.1038/s41477-025-01938-6 | 11760 | GSE270140 | VIB Plant sc-Atlas | Arabidopsis thaliana | ||
| Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase | Ma F, Salomé PA, Merchant SS, Pellegrini M | Plant Cell. 2021 May 31;33(4):1042-1057. doi: 10.1093/plcell/koab025. | 10.1093/plcell/koab025 | 59933 | GSE157580 | Chlamydomonas reinhardtii | |||
| Single-cell RNA sequencing reveals a key regulator ZmEREB14 affecting shoot apex development and yield formation in maize | Ma L, Zhang N, Liu P, Liang Y, Li R, Yuan G, Zou C, Chen Z, Lübberstedt T, Pan G, Shen Y | Plant Biotechnol J. 2025 Mar;23(3):766-779. doi: 10.1111/pbi.14537. Epub 2024 Dec 4. | 10.1111/pbi.14537 | 12700 | n/a | Zea mays | |||
| Single-Cell RNA Sequencing of Arabidopsis Leaf Tissues Identifies Multiple Specialized Cell Types: Idioblast Myrosin Cells and Potential Glucosinolate-Producing Cells | Maeda T, Sugano SS, Shirakawa M, Sagara M, Ito T, Kondo S, Nagano AJ | Plant Cell Physiol. 2023 Mar 1;64(2):234-247. doi: 10.1093/pcp/pcac167. | 10.1093/pcp/pcac167 | 3264 | DRP009643 | scPlantDB | Arabidopsis thaliana | ||
| A cis-regulatory atlas in maize at single-cell resolution | Marand AP, Chen Z, Gallavotti A, Schmitz RJ* | Yes | Cell. 2021 May 27;184(11):3041-3055.e21. doi: 10.1016/j.cell.2021.04.014. Epub 2021 May 7. | 10.1016/j.cell.2021.04.014 | 15515 | GSE155178 | Zea mays | ||
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| A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation | Miller CN, Jarrell-Hurtado S, Haag MV, Sara Ye Y, Simenc M, Alvarez-Maldonado P, Behnami S, Zhang L, Swift J, Papikian A, Yu J, Colt K, Ecker JR*, Michael TP, Law JA, Busch W | Yes | Dev Cell. 2025 Jan 6:S1534-5807(24)00764-0. doi: 10.1016/j.devcel.2024.12.025. Online ahead of print. | 10.1016/j.devcel.2024.12.025 | 19755 | GSE261441 | Arabidopsis thaliana | ||
| Transcriptomics of Arabidopsis sperm cells at single-cell resolution | Misra CS, Santos MR, Rafael-Fernandes M, Martins NP, Monteiro M, Becker JD | Plant Reprod. 2019 Mar;32(1):29-38. doi: 10.1007/s00497-018-00355-4. Epub 2019 Jan 24. | 10.1007/s00497-018-00355-4 | n/a | n/a | Arabidopsis thaliana | |||
| Defining the developmental program leading to meiosis in maize | Nelms B, Walbot V | Science. 2019 Apr 5;364(6435):52-56. doi: 10.1126/science.aav6428. | 10.1126/science.aav6428 | 144 | SRP164771 | scPlantDB | Zea mays | ||
| A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data | Neumann M, Xu X, Smaczniak C, Schumacher J, Yan W, Blüthgen N, Greb T, Jönsson H, Traas J, Kaufmann K, Muino JM | Nat Commun. 2022 May 20;13(1):2838. doi: 10.1038/s41467-022-30177-y. | 10.1038/s41467-022-30177-y | 7716 | SRP320285 | scPlantDB | Arabidopsis thaliana | ||
| A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis | Nguyen TH, Thiers L, Van Moerkercke A, Bai Y, Fernández-Calvo P, Minne M, Depuydt T, Colinas M*, Verstaen K, Van Isterdael G, Nützmann HW, Osbourn A, Saeys Y*, De Rybel B*, Vandepoele K, Ritter A, Goossens A | Yes | Nat Plants. 2023 Jun;9(6):926-937. doi: 10.1038/s41477-023-01419-8. Epub 2023 May 15. | 10.1038/s41477-023-01419-8 | 9660 | GSE179820, GSE212826 | VIB Plant sc-Atlas | Arabidopsis thaliana | |
| A rare PRIMER cell state in plant immunity | Nobori T*, Monell A, Lee TA, Sakata Y, Shirahama S, Zhou J, Nery JR, Mine A, Ecker JR | Yes | Nature. 2025 Feb;638(8049):197-205. doi: 10.1038/s41586-024-08383-z. Epub 2025 Jan 8. | 10.1038/s41586-024-08383-z | 41994 | GSE226826 | Arabidopsis thaliana | ||
| Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root | Nolan TM*, Vukašinovic N, Hsu CW, Zhang J, Vanhoutte I, Shahan R*, Taylor IW, Greenstreet L, Heitz M, Afanassiev A, Wang P, Szekely P, Brosnan A, Yin Y, Schiebinger G, Ohler U, Russinova E, Benfey PN | Yes | Science. 2023 Mar 31;379(6639):eadf4721. doi: 10.1126/science.adf4721. Epub 2023 Mar 31. | 10.1126/science.adf4721 | 210856 | SRP394711 | scPlantDB | Arabidopsis thaliana | |
| WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus | Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M | Sci Adv. 2023 Jul 7;9(27):eadg6983. doi: 10.1126/sciadv.adg6983. Epub 2023 Jul 7. | 10.1126/sciadv.adg6983 | n/a | GSE227564 | Arabidopsis thaliana | |||
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| Ground tissue circuitry regulates organ complexity in maize and Setaria | Ortiz-Ramírez C, Guillotin B*, Xu X, Rahni R, Zhang S, Yan Z, Coqueiro Dias Araujo P, Demesa-Arevalo E, Lee L, Van Eck J, Gingeras TR, Jackson D* , Gallagher KL, Birnbaum KD* | Yes | Science. 2021 Dec 3;374(6572):1247-1252. doi: 10.1126/science.abj2327. Epub 2021 Dec 2. | 10.1126/science.abj2327 | 14733 | SRP145013 | scPlantDB | Zea mays | |
| A root phloem pole cell atlas reveals common transcriptional states in protophloem-adjacent cells | Otero S, Gildea I, Roszak P, Lu Y, Di Vittori V, Bourdon M, Kalmbach L, Blob B, Heo JO, Peruzzo F, Laux T, Fernie AR*, Tavares H, Helariutta Y | Yes | Nat Plants. 2022 Aug;8(8):954-970. doi: 10.1038/s41477-022-01178-y. Epub 2022 Aug 4. | 10.1038/s41477-022-01178-y | 10204 | SRP332285 | scPlantDB | Arabidopsis thaliana | |
| Profiling plant histone modification at single-cell resolution using snCUT&Tag | Ouyang W, Luan S, Xiang X, Guo M, Zhang Y, Li G, Li X | Plant Biotechnol J. 2022 Mar;20(3):420-422. doi: 10.1111/pbi.13768. Epub 2022 Jan 16. | 10.1111/pbi.13768 | 3679 | CRA004386 | Oryza sativa | |||
| The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula | Pereira WJ, Boyd J, Conde D, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Boaventura-Novaes C, Chakraborty S, Knaack SA, Gao Y, Feltus FA, Roy S, Ané JM, Frugoli J, Kirst M | Cell Rep. 2024 Feb 27;43(2):113747. doi: 10.1016/j.celrep.2024.113747. Epub 2024 Feb 7. | 10.1016/j.celrep.2024.113747 | 16824 | GSE224539 | Medicago truncatula | |||
| Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution | Picard CL, Povilus RA, Williams BP, Gehring M | Nat Plants. 2021 Jun;7(6):730-738. doi: 10.1038/s41477-021-00922-0. Epub 2021 May 31. | 10.1038/s41477-021-00922-0 | 1437 | SRP279357 | scPlantDB | Arabidopsis thaliana | ||
| Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection | Procko C, Lee T, Borsuk A, Bargmann BOR, Dabi T, Nery JR, Estelle M, Baird L, O'Connor C, Brodersen | Plant Cell. 2022 Aug 25;34(9):3261-3279. doi: 10.1093/plcell/koac167. | 10.1093/plcell/koac167 | 23729 | SRP338044 | scPlantDB | Arabidopsis thaliana | ||
| Single-cell RNA-seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum) | Qin Y, Sun M, Li W, Xu M, Shao L, Liu Y, Zhao G, Liu Z, Xu Z, You J, Ye Z, Xu J, Yang X, Wang M, Lindsey K, Zhang X, Tu L | Plant Biotechnol J. 2022 Dec;20(12):2372-2388. doi: 10.1111/pbi.13918. Epub 2022 Oct 2. | 10.1111/pbi.13918 | 14535 | SRP241596 | scPlantDB | Gossypium hirsutum | ||
| A temporal map of division, chromatin modification, and identity specification in the regenerating root | Rahni R, Guillotin B*, Lee LR, Birnbaum KD* | Yes | NA | 10.1101/2024.01.09.574680 | 64000 | GSE303996 | Arabidopsis thaliana | ||
| Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization | Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, Verstaen K*, Wendrich J, Melnyk CW, Oda Y, Shasha D, Ahnert SE, Saeys Y*, De Rybel B*, Heidstra R, Scheres B, Grossmann G, Mähönen AP, Denninger P, Göttgens B, Sozzani R, Birnbaum KD* | Yes | Science. 2021 Dec 24;374(6575):eaba5531. doi: 10.1126/science.aba5531. Epub 2021 Dec 24. | 10.1126/science.aba5531 | 272 | GSE140778 | Arabidopsis thaliana | ||
| Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells | Ryu KH, Huang L, Kang HM, Schiefelbein J | Plant Physiol. 2019 Apr;179(4):1444-1456. doi: 10.1104/pp.18.01482. Epub 2019 Feb 4. | 10.1104/pp.18.01482 | 46991 | SRP171040 | scPlantDB, SCEA | Arabidopsis thaliana | ||
| A Wox3-patterning module organizes planar growth in grass leaves and ligules | Satterlee JW, Evans LJ, Conlon BR, Conklin P, Martinez-Gomez J, Yen JR, Wu H, Sylvester AW, Specht CD, Cheng J, Johnston R, Coen E, Scanlon MJ | Nat Plants. 2023 May;9(5):720-732. doi: 10.1038/s41477-023-01405-0. Epub 2023 May 4. | 10.1038/s41477-023-01405-0 | 17128 | SRP417893 | scPlantDB | Zea mays | ||
| Plant stem-cell organization and differentiation at single-cell resolution | Satterlee JW, Strable J, Scanlon MJ | Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33689-33699. doi: 10.1073/pnas.2018788117. Epub 2020 Dec 14. | 10.1073/pnas.2018788117 | 16055 | SRP266308_1, SRP266308_2 | scPlantDB_1, scPlantDB_2 | Zea mays | ||
| Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis | Serrano K, Bezrutczyk M, Goudeau D, Dao T, O'Malley R*, Malmstrom RR, Visel A, Scheller HV, Cole B* | Yes | Nat Plants. 2024 Apr;10(4):673-688. doi: 10.1038/s41477-024-01666-3. Epub 2024 Apr 8. | 10.1038/s41477-024-01666-3 | 38096 | GSE240107 | Medicago truncatula | ||
| Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation | Serrano-Ron L, Perez-Garcia P, Sanchez-Corrionero A, Gude I, Cabrera J, Ip PL, Birnbaum KD* , Moreno-Risueno MA | Yes | Mol Plant. 2021 Aug 2;14(8):1362-1378. doi: 10.1016/j.molp.2021.05.028. Epub 2021 May 29. | 10.1016/j.molp.2021.05.028 | 573 | SRP293943 | scPlantDB | Arabidopsis thaliana | |
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| High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types | Shulse CN, Cole BJ*, Ciobanu D, Lin J, Yoshinaga Y, Gouran M, Turco GM, Zhu Y, O'Malley RC*, Brady SM*, Dickel DE | Yes | Cell Rep. 2019 May 14;27(7):2241-2247.e4. doi: 10.1016/j.celrep.2019.04.054. | 10.1016/j.celrep.2019.04.054 | 12198 | SRP169576 | scPlantDB, SCEA_1, SCEA_2 | Arabidopsis thaliana | |
| Single-cell transcriptome sequencing atlas of cassava tuberous root | Song J, Fan B, Shao X, Zang Y, Wang D, Min Y | Front Plant Sci. 2023 Jan 4;13:1053669. doi: 10.3389/fpls.2022.1053669. eCollection 2022. | 10.3389/fpls.2022.1053669 | 14566 | SRP406470 | scPlantDB | Manihot esculenta | ||
| Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes | Song Q, Ando A, Jiang N, Ikeda Y, Chen ZJ | Genome Biol. 2020 Jul 22;21(1):178. doi: 10.1186/s13059-020-02094-0. | 10.1186/s13059-020-02094-0 | 46 | SRP160651 | SCEA | Arabidopsis thaliana | ||
| Single-Cell RNA-Sequencing of Soybean Reveals Transcriptional Changes and Antiviral Functions of GmGSTU23 and GmGSTU24 in Response to Soybean Mosaic Virus | Song S, Wang J, Zhou J, Cheng X, Hu Y, Wang J, Zou J, Zhao Y, Liu C, Hu Z, Chen Q, Xin D | Plant Cell Environ. 2024 Sep 20. doi: 10.1111/pce.15164. Online ahead of print. | 10.1111/pce.15164 | 50294 | n/a | Glycine max | |||
| A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean | Sun B, Wang Y, Yang Q, Gao H, Niu H, Li Y, Ma Q, Huan Q, Qian W, Ren B | J Integr Plant Biol. 2023 Jun;65(6):1536-1552. doi: 10.1111/jipb.13495. Epub 2023 May 22. | 10.1111/jipb.13495 | 42775 | PRJCA015369 | Glycine max | |||
| Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism | Sun S, Shen X, Li Y, Li Y, Wang S, Li R, Zhang H, Shen G, Guo B, Wei J, Xu J, St-Pierre B, Chen S, Sun C | Nat Plants. 2023 Jan;9(1):179-190. doi: 10.1038/s41477-022-01291-y. Epub 2022 Dec 15. | 10.1038/s41477-022-01291-y | 41981 | SRP335448 | scPlantDB | Catharanthus roseus | ||
| Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage | Sun X, Feng D, Liu M, Qin R, Li Y, Lu Y, Zhang X, Wang Y, Shen S, Ma W, Zhao J | Genome Biol. 2022 Dec 19;23(1):262. doi: 10.1186/s13059-022-02834-4. | 10.1186/s13059-022-02834-4 | 47297 | CRA008834 | Brassica rapa ssp. pekinensis | |||
| Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development | Sun X, Qin A, Wang X, Ge X, Liu Z, Guo C, Yu X, Zhang X, Lu Y, Yang J, He J, Zhou Y, Liu Y, Hu M, Liu H, Zhao Z, Hu G, Li W, Zang X, Dai S, Sun S, Yong-Villalobos L, Herrera-Estrella L, Tran LP, Ma X | Nat Commun. 2025 Jan 20;16(1):858. doi: 10.1038/s41467-025-55869-z. | 10.1038/s41467-025-55869-z | n/a | PRJNA800600 | Gossypium hirsutum | |||
| Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation | Sun Y, Dong L, Kang L, Zhong W, Jackson D* , Yang F | Yes | Mol Plant. 2024 Jul 1;17(7):1019-1037. doi: 10.1016/j.molp.2024.06.007. Epub 2024 Jun 13. | 10.1016/j.molp.2024.06.007 | 56854 | GSE247571 | Zea mays | ||
| Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii | Sun Y, Han Y, Sheng K, Yang P, Cao Y, Li H, Zhu QH, Chen J, Zhu S, Zhao T | Mol Plant. 2023 Apr 3;16(4):694-708. doi: 10.1016/j.molp.2023.02.005. Epub 2023 Feb 10. | 10.1016/j.molp.2023.02.005 | 12222 | SRP424189 | scPlantDB | Gossypium bickii | ||
| Single-cell RNA-seq of Lotus japonicus provide insights into identification and function of root cell types of legume | Sun Z, Jiang S, Wang D, Li L, Liu B, Ran Q, Hu L, Xiong J, Tang Y, Gu X, Wu Y, Liang Z | J Integr Plant Biol. 2023 May;65(5):1147-1152. doi: 10.1111/jipb.13435. Epub 2023 Jan 31. | 10.1111/jipb.13435 | 22688 | SRP376509 | Lotus japonicus | |||
| Single-nucleus RNA sequencing of plant tissues using a nanowell-based system | Sunaga-Franze DY, Muino JM, Braeuning C, Xu X, Zong M, Smaczniak C, Yan W, Fischer C, Vidal R, Kliem M, Kaufmann K, Sauer S | Plant J. 2021 Nov;108(3):859-869. doi: 10.1111/tpj.15458. Epub 2021 Sep 15. | 10.1111/tpj.15458 | 856 | E-MTAB-9174 | Arabidopsis thaliana | |||
| Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics | Tang B, Feng L, Hulin MT, Ding P, Ma W | Cell Host Microbe. 2023 Oct 11;31(10):1732-1747.e5. doi: 10.1016/j.chom.2023.08.019. Epub 2023 Sep 22. | 10.1016/j.chom.2023.08.019 | 102486 | PRJEB61052 | Arabidopsis thaliana | |||
| Single-Cell Transcriptome and Network Analyses Unveil Key Transcription Factors Regulating Mesophyll Cell Development in Maize | Tao S, Liu P, Shi Y, Feng Y, Gao J, Chen L, Zhang A, Cheng X, Wei H, Zhang T, Zhang W | Genes (Basel). 2022 Feb 20;13(2):374. doi: 10.3390/genes13020374. | 10.3390/genes13020374 | 7354 | SRP224648 | scPlantDB | Zea mays | ||
| Arabidopsis uses a molecular grounding mechanism and a biophysical circuit breaker to limit floral abscission signaling | Taylor IW, Patharkar OR, Mijar M, Hsu CW, Baer J, Niederhuth CE, Ohler U, Benfey PN, Walker JC | Proc Natl Acad Sci U S A. 2024 Oct 29;121(44):e2405806121. doi: 10.1073/pnas.2405806121. Epub 2024 Oct 25. | 10.1073/pnas.2405806121 | 40666 | PRJNA857332 | Arabidopsis thaliana | |||
| Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics | Tenorio Berrío R, Verhelst E, Eekhout T, Grones C, De Veylder L, De Rybel B, Dubois M | New Phytol. 2025 Mar 3. doi: 10.1111/nph.20446. Online ahead of print. | 10.1111/nph.20446 | 152793 | GSE273033 | VIB Plant sc-Atlas | Arabidopsis thaliana | ||
| Single-cell transcriptomics sheds light on the identity and metabolism of developing leaf cells | Tenorio Berrío R, Verstaen K, Vandamme N, Pevernagie J, Achon I, Van Duyse J, Van Isterdael G, Saeys Y, De Veylder L, Inzé D, Dubois M | Plant Physiol. 2022 Feb 4;188(2):898-918. doi: 10.1093/plphys/kiab489. | 10.1093/plphys/kiab489 | 1887 | ERP132245 | SCEA | Arabidopsis thaliana | ||
| Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex | Tian C, Du Q, Xu M, Du F, Jiao Y | NA | 10.1101/2020.09.20.305029 | 64640 | PRJNA661700 | SCEA_1, SCEA_2 | Solanum lycopersicum | ||
| A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing | Torii K, Inoue K, Bekki K, Haraguchi K, Kubo M, Kondo Y, Suzuki T, Kubota A, Uemoto K, Shimizu H, Saito M, Fukuda H, Araki T, Endo M | Cell Rep. 2022 Jul 12;40(2):111059. doi: 10.1016/j.celrep.2022.111059. | 10.1016/j.celrep.2022.111059 | n/a | PRJNA551314 | Arabidopsis thaliana | |||
| A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells | Tu X, Marand AP, Schmitz RJ* , Zhong S | Yes | Plant Commun. 2022 Jul 11;3(4):100308. doi: 10.1016/j.xplc.2022.100308. Epub 2022 Mar 2. | 10.1016/j.xplc.2022.100308 | 13576 | GSE155304 (previously published) | Arabidopsis thaliana | ||
| Single-cell transcriptomics unveils xylem cell development and evolution | Tung CC, Kuo SC, Yang CL, Yu JH, Huang CE, Liou PC, Sun YH, Shuai P, Su JC, Ku C, Lin YJ | Genome Biol. 2023 Jan 9;24(1):3. doi: 10.1186/s13059-022-02845-1. | 10.1186/s13059-022-02845-1 | 25166 | GSE180121 | Populus trichocarpa | |||
| Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation | Turco GM, Rodriguez-Medina J, Siebert S, Han D, Valderrama-Gómez MÁ, Vahldick H, Shulse CN, Cole BJ*, Juliano CE, Dickel DE, Savageau MA, Brady SM* | Yes | Cell Rep. 2019 Jul 9;28(2):342-351.e4. doi: 10.1016/j.celrep.2019.06.041. | 10.1016/j.celrep.2019.06.041 | 6727 | SRP148288 | scPlantDB, SCEA | Arabidopsis thaliana | |
| Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells | Vukašinovic N, Hsu CW, Marconi M, Li S, Zachary C, Shahan R*, Szekley P, Aardening Z, Vanhoutte I, Ma Q, Pinto L, Krupar P, German N, Zhang J, Simon-Vezo C, Perez-Sancho J, Quijada PC, Zhou Q, Lee LR, Cai J, Bayer EM, Fendrych M, Truernit E, Zhou Y, Savaldi-Goldstein S, Wabnik K, Nolan TM*, Russinova E | Yes | Cell. 2025 Mar 6:S0092-8674(25)00196-5. doi: 10.1016/j.cell.2025.02.011. Online ahead of print. | 10.1016/j.cell.2025.02.011 | 157175 | GSE262840 | Arabidopsis thaliana | ||
| Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton | Wang D, Hu X, Ye H, Wang Y, Yang Q, Liang X, Wang Z, Zhou Y, Wen M, Yuan X, Zheng X, Ye W, Guo B, Yusuyin M, Russinova E, Zhou Y, Wang K | Genome Biol. 2023 Mar 14;24(1):49. doi: 10.1186/s13059-023-02886-0. | 10.1186/s13059-023-02886-0 | 39453 | SRP379192 | scPlantDB | Gossypium hirsutum | ||
| Single-cell-type transcriptomic analysis reveals distinct gene expression profiles in wheat guard cells in response to abscisic acid | Wang J, Li Y, Wu T, Miao C, Xie M, Ding B, Li M, Bao S, Chen X, Hu Z, Xie X | Funct Plant Biol. 2021 Oct;48(11):1087-1099. doi: 10.1071/FP20368. | 10.1071/FP20368 | n/a | n/a (not really single cell) | Triticum aestivum | |||
| An optimized FACS-free single-nucleus RNA sequencing (snRNA-seq) method for plant science research | Wang K, Zhao C, Xiang S, Duan K, Chen X, Guo X, Sahu SK | Plant Sci. 2023 Jan;326:111535. doi: 10.1016/j.plantsci.2022.111535. Epub 2022 Nov 16. | 10.1016/j.plantsci.2022.111535 | 19171 | CNP0002469 | Arabidopsis thaliana | |||
| The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution | Wang L, Wan MC, Liao RY, Xu J, Xu ZG, Xue HC, Mai YX, Wang JW | Dev Cell. 2023 Aug 7;58(15):1429-1444.e6. doi: 10.1016/j.devcel.2023.05.014. Epub 2023 Jun 14. | 10.1016/j.devcel.2023.05.014 | 46136 | PRJCA013186 | Marchantia polymorpha | |||
| Single cell-type transcriptome profiling reveals genes that promote nitrogen fixation in the infected and uninfected cells of legume nodules | Wang L, Zhou Y, Li R, Liang J, Tian T, Ji J, Chen R, Zhou Y, Fan Q, Ning G, Larkin RM, Becana M, Duanmu D | Plant Biotechnol J. 2022 Apr;20(4):616-618. doi: 10.1111/pbi.13778. Epub 2022 Jan 31. | 10.1111/pbi.13778 | n/a | GSE188748 | Lotus japonicus | |||
| Histological and single-nucleus transcriptome analyses reveal the specialized functions of ligular sclerenchyma cells and key regulators of leaf angle in maize | Wang Q, Guo Q, Shi Q, Yang H, Liu M, Niu Y, Quan S, Xu D, Chen X, Li L, Xu W, Kong F, Zhang H, Li P, Li B, Li G | Mol Plant. 2024 Jun 3;17(6):920-934. doi: 10.1016/j.molp.2024.05.001. Epub 2024 May 7. | 10.1016/j.molp.2024.05.001 | 7049 | PRJCA020760 | Zea mays | |||
| Single-cell transcriptome atlas reveals developmental trajectories and a novel metabolic pathway of catechin esters in tea leaves | Wang Q, Wu Y, Peng A, Cui J, Zhao M, Pan Y, Zhang M, Tian K, Schwab W, Song C | Plant Biotechnol J. 2022 Nov;20(11):2089-2106. doi: 10.1111/pbi.13891. Epub 2022 Jul 26. | 10.1111/pbi.13891 | 16977 | n/a | Camellia sinensis | |||
| ScRNA-seq reveals the spatiotemporal distribution of camptothecin pathway and transposon activity in Camptotheca acuminata shoot apexes and leaves | Wang S, Zhang C, Li Y, Li R, Du K, Sun C, Shen X, Guo B | Physiol Plant. 2024 Sep-Oct;176(5):e14508. doi: 10.1111/ppl.14508. | 10.1111/ppl.14508 | 74858 | PRJCA023356 | Camptotheca acuminata | |||
| Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots | Wang T, Wang F, Deng S, Wang K, Feng D, Xu F, Guo W, Yu J, Wu Y, Wuriyanghan H, Li ST, Gu X, Le L, Pu L | Nat Commun. 2025 Jan 2;16(1):177. doi: 10.1038/s41467-024-55485-3. | 10.1038/s41467-024-55485-3 | 35103 | CRA015077 | Zea mays | |||
| Integration of single-nuclei transcriptome and bulk RNA-seq to unravel the role of AhWRKY70 in regulating stem cell development in Arachis hypogaea L | Wang X, Wang R, Huo X, Zhou Y, Umer MJ, Zheng Z, Jin W, Huang L, Li H, Yu Q, Li S, Varshney RK, Wang W, Xiao Y, Hong Y, Chen X, Lu Q, Liu H | Plant Biotechnol J. 2025 Mar 13. doi: 10.1111/pbi.70009. Online ahead of print. | 10.1111/pbi.70009 | 29308 | CRA014837 | Arachis hypogaea | |||
| Single-cell transcriptome atlas of the leaf and root of rice seedlings | Wang Y, Huan Q, Li K, Qian W | J Genet Genomics. 2021 Oct 20;48(10):881-898. doi: 10.1016/j.jgg.2021.06.001. Epub 2021 Jun 18. | 10.1016/j.jgg.2021.06.001 | 232384 | CRA004082 | scPlantDB | Oryza sativa | ||
| A spatial transcriptome map of the developing maize ear | Wang Y, Luo Y, Guo X, Li Y, Yan J, Shao W, Wei W, Wei X, Yang T, Chen J, Chen L, Ding Q, Bai M, Zhuo L, Li L, Jackson D*, Zhang Z, Xu X, Yan J, Liu H, Liu L, Yang N | Yes | Nat Plants. 2024 May;10(5):815-827. doi: 10.1038/s41477-024-01683-2. Epub 2024 May 14. | 10.1038/s41477-024-01683-2 | 19584 | CNP0004249 | Zea mays | ||
| Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions | Wendrich JR, Yang B, Vandamme N, Verstaen K, Smet W, Van de Velde C, Minne M, Wybouw B, Mor E, Arents HE, Nolf J, Van Duyse J, Van Isterdael G, Maere S, Saeys Y*, De Rybel B* | Yes | Science. 2020 Nov 13;370(6518):eaay4970. doi: 10.1126/science.aay4970. Epub 2020 Sep 17. | 10.1126/science.aay4970 | 15918 | SRP235541 | scPlantDB, SCEA | Arabidopsis thaliana | |
| Identification of bZIP Transcription Factors That Regulate the Development of Leaf Epidermal Cells in Arabidopsis thaliana by Single-Cell RNA Sequencing | Wu R, Liu Z, Sun S, Qin A, Liu H, Zhou Y, Li W, Liu Y, Hu M, Yang J, Rochaix JD, An G, Herrera-Estrella L, Tran LP, Sun X | Int J Mol Sci. 2024 Feb 22;25(5):2553. doi: 10.3390/ijms25052553. | 10.3390/ijms25052553 | 18000 | PRJNA577177 | Arabidopsis thaliana | |||
| Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John's wort | Wu S, Morotti ALM, Yang J, Wang E, Tatsis EC | Mol Plant. 2024 Sep 2;17(9):1439-1457. doi: 10.1016/j.molp.2024.08.003. Epub 2024 Aug 12. | 10.1016/j.molp.2024.08.003 | 15074 | PRJNA1060879 | Hypericum perforatum | |||
| The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves | Xia K, Sun HX, Li J, Li J, Zhao Y, Chen L, Qin C, Chen R, Chen Z, Liu G, Yin R, Mu B, Wang X, Xu M, Li X, Yuan P, Qiao Y, Hao S, Wang J*, Xie Q, Xu J, Liu S, Li Y, Chen A, Liu L, Yin Y, Yang H, Wang J*, Gu Y, Xu X | Yes | Dev Cell. 2022 May 23;57(10):1299-1310.e4. doi: 10.1016/j.devcel.2022.04.011. Epub 2022 May 4. | 10.1016/j.devcel.2022.04.011 | n/a (spatial) | CNP0002618 | scPlantDB | Arabidopsis thaliana | |
| Single-cell RNA sequencing profiles of stem-differentiating xylem in poplar | Xie J, Li M, Zeng J, Li X, Zhang D | Plant Biotechnol J. 2022 Mar;20(3):417-419. doi: 10.1111/pbi.13763. Epub 2021 Dec 23. | 10.1111/pbi.13763 | 12466 | n/a | Populus trichocarpa | |||
| Single-Cell RNA Sequencing Efficiently Predicts Transcription Factor Targets in Plants | Xie Y, Jiang S, Li L, Yu X, Wang Y, Luo C, Cai Q, He W, Xie H, Zheng Y, Xie H, Zhang J | Front Plant Sci. 2020 Dec 8;11:603302. doi: 10.3389/fpls.2020.603302. eCollection 2020. | 10.3389/fpls.2020.603302 | 16527 | SRP286275 | scPlantDB | Oryza sativa | ||
| The soil emergence-related transcription factor PIF3 controls root penetration by interacting with the receptor kinase FER | Xu F, Chen J, Li Y, Ouyang S, Yu M, Wang Y, Fang X, He K, Yu F | Dev Cell. 2024 Feb 26;59(4):434-447.e8. doi: 10.1016/j.devcel.2024.01.001. Epub 2024 Jan 30. | 10.1016/j.devcel.2024.01.001 | 70905 | GSE225299 | Arabidopsis thaliana | |||
| Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery | Xu X, Crow M, Rice BR, Li F, Harris B, Liu L, Demesa-Arevalo E, Lu Z, Wang L, Fox N, Wang X, Drenkow J, Luo A, Char SN, Yang B, Sylvester AW, Gingeras TR, Schmitz RJ*, Ware D, Lipka AE, Gillis J, Jackson D* | Yes | Dev Cell. 2021 Feb 22;56(4):557-568.e6. doi: 10.1016/j.devcel.2020.12.015. Epub 2021 Jan 4. | 10.1016/j.devcel.2020.12.015 | 12525 | SRP272727_23_26 | scPlantDB, SCEA | Zea mays | |
| Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation | Xu X, Passalacqua M*, Rice B, Demesa-Arevalo E, Kojima M, Takebayashi Y, Harris B, Sakakibara H, Gallavotti A, Gillis J, Jackson D* | Yes | Dev Cell. 2025 Aug 25:S1534-5807(25)00500-3 | 10.1016/j.devcel.2025.07.024 | 11554 | PRJNA1039503, PRJNA1039507, PRJNA1036155, PRJNA1036156 | Zea mays | ||
| Evolution of plant cell-type-specific cis-regulatory elements | Yan H, Mendieta JP, Zhang X, Marand AP, Liang Y, Luo Z, Minow MAA, Jang H, Li X, Roule T, Wagner D, Tu X, Wang Y, Jiang D, Zhong S, Huang L, Wessler SR, Schmitz RJ* | Yes | bioRxiv [Preprint]. 2024 Oct 5:2024.01.08.574753. doi: 10.1101/2024.01.08.574753. | 10.1101/2024.01.08.574753 | 57552 | PRJNA1052039, GSE252040 | Zea mays, Sorghum bicolor, Panicum miliaceum, Urochloa fusca | ||
| Single-cell transcriptomic profiling of maize cell heterogeneity and systemic immune responses against Puccinia polysora Underw | Yan XC, Liu Q, Yang Q, Wang KL, Zhai XZ, Kou MY, Liu JL, Li ST, Deng SH, Li MM, Duan HJ | Plant Biotechnol J. 2025 Feb;23(2):549-563. doi: 10.1111/pbi.14519. Epub 2024 Nov 29. | 10.1111/pbi.14519 | 70803 | PRJNA1085690 | Zea mays | |||
| Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development | Yang B, Minne M, Brunoni F, Pla?ková L, Pet?ík I, Sun Y, Nolf J, Smet W, Verstaen K*, Wendrich JR*, Eekhout T*, Hoyerová K, Van Isterdael G, Haustraete J, Bishopp A, Farcot E, Novák O, Saeys Y*, De Rybel B* | Yes | Nat Plants. 2021 Nov;7(11):1485-1494. doi: 10.1038/s41477-021-01017-6. Epub 2021 Nov 15. | 10.1038/s41477-021-01017-6 | 10000 | GSE179820 | VIB Plant sc-Atlas | Arabidopsis thaliana | |
| Single-nucleus RNA sequencing and mRNA hybridization indicate key bud events and LcFT1 and LcTFL1-2 mRNA transportability during floral transition in litchi | Yang MC, Wu ZC, Chen RY, Abbas F, Hu GB, Huang XM, Guan WS, Xu YS, Wang HC | J Exp Bot. 2023 Jun 27;74(12):3613-3629. doi: 10.1093/jxb/erad103. | 10.1093/jxb/erad103 | 41641 | PRJNA909160 | Litchi chinensis | |||
| Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination | Yao J, Chu Q, Guo X, Shao W, Shang N, Luo K, Li X, Chen H, Cheng Q, Mo F, Zheng D, Xu F, Guo F, Zhu QH, Deng S, Chu C, Xu X, Liu H, Fan L | Dev Cell. 2024 Sep 9;59(17):2320-2332.e5. doi: 10.1016/j.devcel.2024.05.016. Epub 2024 Jun 6. | 10.1016/j.devcel.2024.05.016 | 27099 | CNP0004152 | Oryza sativa | |||
| Differentiation trajectories and biofunctions of symbiotic and un-symbiotic fate cells in root nodules of Medicago truncatula | Ye Q, Zhu F, Sun F, Wang T, Wu J, Liu P, Shen C, Dong J, Wang T | NA | 10.1016/j.molp.2022.10.019 | 9756 | PRJCA012129 | Medicago truncatula | |||
| A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis | Yin R, Chen R, Xia K, Xu X | Plant Commun. 2024 Aug 12;5(8):100941. doi: 10.1016/j.xplc.2024.100941. Epub 2024 May 7. | 10.1016/j.xplc.2024.100941 | 25188 | CNP0004389 | Arabidopsis thaliana | |||
| Integrated mass spectrometry imaging and single-cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems | Yu C, Hou K, Zhang H, Liang X, Chen C, Wang Z, Wu Q, Chen G, He J, Bai E, Li X, Du T, Wang Y, Wang M, Feng S, Wang H, Shen C | Plant J. 2023 Sep;115(5):1243-1260. doi: 10.1111/tpj.16315. Epub 2023 Jun 2. | 10.1111/tpj.16315 | 21233 | PRJNA730337 | Taxus mairei | |||
| Single-cell atlases reveal leaf cell-type-specific regulation of metal transporters in the hyperaccumulator Sedum alfredii under cadmium stress | Yu G, Xiang J, Liu J, Zhang X, Lin H, Sunahara GI, Yu H, Jiang P, Lan H, Qu J | J Hazard Mater. 2024 Dec 5;480:136185. doi: 10.1016/j.jhazmat.2024.136185. Epub 2024 Oct 16. | 10.1016/j.jhazmat.2024.136185 | 12616 | n/a | Sedum alfredii | |||
| Decoding the gene regulatory network of endosperm differentiation in maize | Yuan Y, Huo Q, Zhang Z, Wang Q, Wang J, Chang S, Cai P, Song KM, Galbraith DW, Zhang W, Huang L, Song R, Ma Z | Nat Commun. 2024 Jan 2;15(1):34. doi: 10.1038/s41467-023-44369-7. | 10.1038/s41467-023-44369-7 | 17022 | GSE201701 | Zea mays | |||
| Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf | Yue H, Chen G, Zhang Z, Guo Z, Zhang Z, Zhang S, Turlings TCJ, Zhou X, Peng J, Gao Y, Zhang D, Shi X, Liu Y | Plant Cell Environ. 2024 Jul;47(7):2660-2674. doi: 10.1111/pce.14906. Epub 2024 Apr 15. | 10.1111/pce.14906 | 23226 | GSE201931 | Solanum lycopersicum | |||
| Single-cell RNA-sequencing profiles reveal the developmental landscape of the Manihot esculenta Crantz leaves | Zang Y, Pei Y, Cong X, Ran F, Liu L, Wang C, Wang D, Min Y | Plant Physiol. 2023 Dec 30;194(1):456-474. doi: 10.1093/plphys/kiad500. | 10.1093/plphys/kiad500 | 11177 | CRA012723 | Manihot esculenta | |||
| Single-Cell RNA sequencing of leaf sheath cells reveals the mechanism of rice resistance to brown planthopper (Nilaparvata lugens) | Zha W, Li C, Wu Y, Chen J, Li S, Sun M, Wu B, Shi S, Liu K, Xu H, Li P, Liu K, Yang G, Chen Z, Xu D, Zhou L, You A | Front Plant Sci. 2023 Jun 19;14:1200014. doi: 10.3389/fpls.2023.1200014. eCollection 2023. | 10.3389/fpls.2023.1200014 | 30936 | CRA009555 | Oryza sativa | |||
| Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration | Zhai N, Xu L | Nat Plants. 2021 Nov;7(11):1453-1460. doi: 10.1038/s41477-021-01015-8. Epub 2021 Nov 15. | 10.1038/s41477-021-01015-8 | 5913 | SRP279055 | scPlantDB | Arabidopsis thaliana | ||
| Single-cell RNA-sequencing provides new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass leaf blades | Zhang B, Ma Z, Guo H, Chen S, Liu J | Plant Physiol Biochem. 2024 Aug;213:108857. doi: 10.1016/j.plaphy.2024.108857. Epub 2024 Jun 18. | 10.1016/j.plaphy.2024.108857 | 5296 | PRJNA918429 | Cynodon dactylon | |||
| Spatial transcriptome and single-cell RNA sequencing reveal the molecular basis of cotton fiber initiation development | Zhang J, Chen R, Dai F, Tian Y, Shi Y, He Y, Hu Y, Zhang T | Plant J. 2025 Mar;121(6):e70064. doi: 10.1111/tpj.70064. | 10.1111/tpj.70064 | 7566 | PRJNA869296 | Gossypium hirsutum | |||
| Cell type-specific cytonuclear coevolution in three allopolyploid plant species | Zhang K, Zhao X, Zhao Y, Zhang Z, Liu Z, Liu Z, Yu Y, Li J, Ma Y, Dong Y, Pang X, Jin X, Li N, Liu B, Wendel JF, Zhai J, Long Y, Wang T, Gong L | Proc Natl Acad Sci U S A. 2023 Oct 3;120(40):e2310881120. doi: 10.1073/pnas.2310881120. Epub 2023 Sep 25. | 10.1073/pnas.2310881120 | 2314 | PRJNA985908 | Arachis hypogaea, Gossypium hirsutum, Triticum aestivum | |||
| Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis | Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W | Genome Biol. 2023 Apr 4;24(1):65. doi: 10.1186/s13059-023-02908-x. | 10.1186/s13059-023-02908-x | 6875 | CRA008788 | scPlantDB | Triticum aestivum | ||
| Single-cell RNA sequencing analysis of the embryogenic callus clarifies the spatiotemporal developmental trajectories of the early somatic embryo in Dimocarpus longan | Zhang S, Zhu C, Zhang X, Liu M, Xue X, Lai C, Xuhan X, Chen Y, Zhang Z, Lai Z, Lin Y | Plant J. 2023 Sep;115(5):1277-1297. doi: 10.1111/tpj.16319. Epub 2023 Jun 9. | 10.1111/tpj.16319 | 28727 | PRJCA016297, PRJCA016314, PRJCA016317 | Dimocarpus longan | |||
| Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root | Zhang TQ, Chen Y, Liu Y, Lin WH, Wang JW | Nat Commun. 2021 Apr 6;12(1):2053. doi: 10.1038/s41467-021-22352-4. | 10.1038/s41467-021-22352-4 | 28857 | SRP309176 | scPlantDB, SCEA | Oryza sativa | ||
| A single-cell analysis of the Arabidopsis vegetative shoot apex | Zhang TQ, Chen Y, Wang JW | Dev Cell. 2021 Apr 5;56(7):1056-1074.e8. doi: 10.1016/j.devcel.2021.02.021. Epub 2021 Mar 15. | 10.1016/j.devcel.2021.02.021 | 36643 | CRA002977_1, CRA002977_2 | scPlantDB_1, scPlantDB_2, SCEA | Arabidopsis thaliana | ||
| A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root | Zhang TQ, Xu ZG, Shang GD, Wang JW | Mol Plant. 2019 May 6;12(5):648-660. doi: 10.1016/j.molp.2019.04.004. Epub 2019 Apr 17. | 10.1016/j.molp.2019.04.004 | 7695 | SRP182008 | scPlantDB | Arabidopsis thaliana | ||
| A spatially resolved multi-omic single-cell atlas of soybean development | Zhang X, Luo Z, Marand AP, Yan H, Jang H, Bang S, Mendieta JP, Minow MAA, Schmitz RJ* | Yes | Cell. 2025 Jan 23;188(2):550-567.e19. doi: 10.1016/j.cell.2024.10.050. Epub 2024 Dec 31. | 10.1016/j.cell.2024.10.050 | 310814 | GSE270392 | Soybean Atlas | Glycine max | |
| Transcriptional landscape of sweetpotato root tip development at the single-cell level | Zhao N, Ding X, Tian C, Wang S, Xie S, Zou H, Liu H, Chen J, Lian Liang X, Huang L | BMC Plant Biol. 2024 Oct 12;24(1):952. doi: 10.1186/s12870-024-05574-8. | 10.1186/s12870-024-05574-8 | 13966 | PRJCA020029 | Ipomoea batatas | |||
| Single-cell RNA-seq reveals a link of ovule abortion and sugar transport in Camellia oleifera | Zhao S, Rong J | Front Plant Sci. 2024 Feb 2;15:1274013. doi: 10.3389/fpls.2024.1274013. eCollection 2024. | 10.3389/fpls.2024.1274013 | 20526 | PRJCA018533 | Camellia oleifera | |||
| Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes | Zhou P, Chen H, Dang J, Shi Z, Shao Y, Liu C, Fan L, Wu Q | Front Plant Sci. 2022 Oct 19;13:988594. doi: 10.3389/fpls.2022.988594. eCollection 2022. | 10.3389/fpls.2022.988594 | 33299 | PRJNA743551 | Nepeta tenuifolia | |||
| Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection | Zhu J, Lolle S, Tang A, Guel B, Kvitko B, Cole B*, Coaker G | Yes | Cell Rep. 2023 Jul 25;42(7):112676. doi: 10.1016/j.celrep.2023.112676. Epub 2023 Jun 20. | 10.1016/j.celrep.2023.112676 | 11896 | GSE213625 | Arabidopsis thaliana | ||
| Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem | Zhu X, Xu Z, Wang G, Cong Y, Yu L, Jia R, Qin Y, Zhang G, Li B, Yuan D, Tu L, Yang X, Lindsey K, Zhang X, Jin S | Genome Biol. 2023 Aug 25;24(1):194. doi: 10.1186/s13059-023-03032-6. | 10.1186/s13059-023-03032-6 | 59591 | PRJNA895968, PRJNA895970 | Jin Lab Viewer | Gossypium hirsutum | ||
| A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems | Zong J, Wang L, Zhu L, Bian L, Zhang B, Chen X, Huang G, Zhang X, Fan J, Cao L, Coupland G, Liang W, Zhang D, Yuan Z | New Phytol. 2022 Apr;234(2):494-512. doi: 10.1111/nph.18008. Epub 2022 Feb 24. | 10.1111/nph.18008 | 37571 | SRP339472 | scPlantDB | Oryza sativa |