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| Status |
Public on Dec 31, 2020 |
| Title |
Single cell RNA sequencing of Col-0 leaf cell |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about the vascular cells in leaves, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading; yet PP has only been characterized microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified ?19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. PP development occurs independently from APL, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CC), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our scRNA-seq analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
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| Overall design |
We enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature.
Two biological replicates were performed with the aim of capturing ~7,000 leaf protoplasts for each replicate. Freshly isolated protoplasts were loaded into the 10X Genomics Chromium single cell microfluidics device according to the Single Cell 3’ Reagent Kit v2 protocol. scRNA-seq library sequencing was performed on a NextSeq platform.
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| Contributor(s) |
Kim J, Symeonidi E, Pang TY, Denyer T, Weidauer D, Bezrutczyk M, Miras M, Zöllner N, Wudick MM, Hartwig T, Wudick MM, Lercher M, Chen L, Timmermans MC, Frommer WB |
| Citation(s) |
33955487 |
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| Submission date |
Nov 12, 2020 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Jiyun Kim |
| Organization name |
HHU
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| Department |
Biology
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| Lab |
Institute of Molecular Physiology
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| Street address |
Universitätsstr. 1
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| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE161482 |
Unique and distinct identities and functions of leaf phloem cells revealed by single cell transcriptomics |
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| Relations |
| BioProject |
PRJNA677901 |
| SRA |
SRP292306 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE161332_barcodes.tsv.gz |
26.3 Kb |
(ftp)(http) |
TSV |
| GSE161332_features.tsv.gz |
172.7 Kb |
(ftp)(http) |
TSV |
| GSE161332_matrix.mtx.gz |
54.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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