GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE161332 Query DataSets for GSE161332
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
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.
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.
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
Submission date Nov 12, 2020
Last update date Jun 03, 2021
Contact name Jiyun Kim
Organization name HHU
Department Biology
Lab Institute of Molecular Physiology
Street address Universitätsstr. 1
City Düsseldorf
ZIP/Postal code 40225
Country Germany
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (2)
GSM4905002 Leaf protoplast scRNA seq- Library 1
GSM4905003 Leaf protoplast scRNA seq- Library 2
This SubSeries is part of SuperSeries:
GSE161482 Unique and distinct identities and functions of leaf phloem cells revealed by single cell transcriptomics
BioProject PRJNA677901
SRA SRP292306

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap