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Series GSE224928 Query DataSets for GSE224928
Status Public on Apr 04, 2023
Title Transcriptome of radially growing Arabidopsis wild type and d14 mutant hypocotyls with single cell resolution revealed by nucleus RNA-seq using 10x Chomium and VASA-seq
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Wood formation is fundamental for the remarkable growth of plant bodies by continuously providing cells for long-distance transport of water and nutrients and for mechanical support. Vessel elements, the water transporting units within woody tissues, are generated from a cylindrical domain of cambium stem cells (CSCs) generating different vascular cell types in a bidirectional manner during the radial (secondary) growth. However, knowledge on the regulation of CSC activity is limited with unclear cell fate trajectories as the most obscure aspect in this context. Here, we provide a transcriptome atlas of CSCs and their derivatives at single cell resolution in Arabidopsis thaliana hypocotyl.
 
Overall design Nuclei of Arabidopsis thaliana (wild type, PXY:H4-GFP;SMXL5:H2B-RFP) hypocotyls were isolated by Fluorescence-activated nucleus sorting (FANS) based on Hoechst staining and analyzed using snRNAseq by the 10x Genomics pipeline (Library: DSNucseq2). Furthermore, VASA-seq analyses in 384-well plate format were applied to nuclei from whole hypocotyls (three replicate plates, Library: UHE-DS-v011, 012, 013) and cambium enriched nuclei (three replicate plates, Library: UHE-DS-v008, v009, v010) according to the GFP and RFP signal of nuclei during FANS (GFP+ and/or RFP+ nuclei). In addition, hypocotyl nuclei of wild type and d14-1 mutants were isolated and analyzed using snRNAseq by the 10x Genomics pipeline (Library: WT, d14).
Web link https://doi.org/10.1101/2023.04.05.535530
 
Contributor(s) Dongbo S, Jiao Z, Changzheng S, Thomas G
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Submission date Feb 09, 2023
Last update date Jul 06, 2023
Contact name Thomas Greb
E-mail(s) thomas.greb@cos.uni-heidelberg.de
Organization name Heidelberg University
Department Centre for Organismal Studies
Lab Greb
Street address Im Neuenheimer Feld 360
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platforms (2)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL24270 NextSeq 550 (Arabidopsis thaliana)
Samples (9)
GSM7035821 10x_all_hypocotyl, snRNAseq
GSM7035822 VASA_cambium, rep1, snRNAseq
GSM7035823 VASA_cambium, rep2, snRNAseq
Relations
BioProject PRJNA933135

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
GSE224928_10x-all_hypocotyl_barcodes.tsv.gz 17.5 Mb (ftp)(http) TSV
GSE224928_10x-all_hypocotyl_features.tsv.gz 201.3 Kb (ftp)(http) TSV
GSE224928_RAW.tar 160.9 Mb (http)(custom) TAR (of MTX)
GSE224928_VASAseq-barcodes.tsv.gz 1.2 Kb (ftp)(http) TSV
GSE224928_VASAseq-features.tsv.gz 201.8 Kb (ftp)(http) TSV
GSE224928_WTd14-10x-barcodes.tsv.gz 3.1 Mb (ftp)(http) TSV
GSE224928_WTd14-10x-features.tsv.gz 193.9 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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