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Series GSE121619 Query DataSets for GSE121619
Status Public on Mar 29, 2019
Title Dynamics of gene expression in single root cells of A. thaliana
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Here, we apply this approach to A. thaliana root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single-cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution
Overall design Single-cell RNA-seq experiments were performed on protoplast cells extracted from the whole roots of 7-8 day old Arabidopsis thanliana seedlings. Plants were grown under control conditions at 22C. Plants were moved from 22C to 38C for 45 min to be heatshocked.
Please note that the 'whole_root_Control_2' data was aggregated with the 'whole_root_Heatshock data' for comparative analysis.
Contributor(s) Cuperus J, Queitsch C
Citation(s) 30923229
Submission date Oct 22, 2018
Last update date Apr 12, 2020
Contact name Christine Queitsch
Phone 206-685-8935
Organization name University of Washington
Department Genome Sciences
Lab Queitsch Lab
Street address 3720 15th Ave NE, Foege Hall
City Seattle
State/province WA
ZIP/Postal code 98105
Country USA
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (3)
GSM4466787 whole_root_Control_1
GSM4466788 whole_root_Control_2
GSM4466789 whole_root_Heatshock
BioProject PRJNA497883
SRA SRP166333

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE121619_Control_Heatshock_cds.rds.gz 72.6 Mb (ftp)(http) RDS
GSE121619_Control_Heatshock_pData.tsv.gz 47.6 Kb (ftp)(http) TSV
GSE121619_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE121619_genes.tsv.gz 175.1 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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