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Series GSE158761 Query DataSets for GSE158761
Status Public on Jan 01, 2021
Title A single cell view of the transcriptome during lateral root initiation
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Plant root architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can also alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied developmental processes in Arabidopsis thaliana, yet the earliest steps of organogenesis remain elusive. Among the challenges faced in capturing these early molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. The advent of single-cell sequencing affords the opportunity to isolate cells undergoing this fate transition and examine their transcriptomes independently. Using this approach, we successfully captured the transcriptomes of lateral root primordia and discovered many previously unreported upregulated genes. To further study this process, we developed a method to selectively repress genes in the xylem pole pericycle cells where lateral roots originate. We found that expression of several of the upregulated genes was required for normal root development. In addition, we discovered a subpopulation of cells in the endodermal cell file that respond to lateral root initiation, further highlighting the benefits of the single cell approach.
Overall design Using the 10X single cell transcriptomics platform, we isolated cells from Arabidopsis roots to study lateral root formation. To stimulate lateral root formation, Arabidopsis seedlings were rotated 90 degrees and cells from the root bend were captured 08 hours, and 20 hours after the stimulus. Cells from a no bend control, 00 hours, were collected as well.

The RDS files (included on Jan 25, 2021) are the processed Monocle 3 cell data structures, which can be loaded directly into R, to help those trying to reproduce analysis results or those who want to use the UMAPs for further analysis.
Web link http://10.1093/plcell/koab101
Contributor(s) Cuperus JT, Nemhauser JL
Citation(s) 33822225
Submission date Sep 29, 2020
Last update date Apr 06, 2021
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 (7)
GSM4809923 00 hour rep 1
GSM4809924 08 hour rep 1
GSM4809925 20 hour rep 1
BioProject PRJNA666436
SRA SRP285817

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
GSE158761_all_cells_labeled.rds.gz 54.6 Mb (ftp)(http) RDS
GSE158761_barcodes.tsv.gz 44.8 Kb (ftp)(http) TSV
GSE158761_ce_cells_labeled.rds.gz 5.1 Mb (ftp)(http) RDS
GSE158761_genes.tsv.gz 88.0 Kb (ftp)(http) TSV
GSE158761_matrix.mtx.gz 30.9 Mb (ftp)(http) MTX
GSE158761_pericycle_cells_labeled.rds.gz 15.6 Mb (ftp)(http) RDS
GSE158761_stele_cells_labeled.rds.gz 21.4 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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