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Series GSE226826 Query DataSets for GSE226826
Status Public on Apr 24, 2023
Title Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that have a critical impact on plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present an atlas of gene regulatory logic involving transcription factors, potential cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integration of our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic. Overall, this study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.
Overall design Arabidopsis thaliana Col-0 were grown in a chamber at 22°C with a 12-h light period and 60-70% relative humidity for 30-31 days. Bacterial stains were cultured in the King’s B liquid medium with antibiotics (Rifampicin and Tetracyclin) at 28°C. Three bacterial strains–Pseudomonas syringae pv tomato DC3000 (Pto DC3000) carrying empty vector (pLAFR3), avrRpt2 (pLAFR3), and avrRpm1 (pLAFR3)–were described previously (Whalen et al. 1991; Kunkel et al. 1993). Bacteria were harvested by centrifugation and resuspended in sterile water to an OD600 of 0.001 (approximately 5 x 105 CFU ml-1). In total, 20 A. thaliana leaves (four fully-expanded leaves per plant) were syringe-inoculated with bacterial suspensions using a needleless syringe. For each strain, four time points (4, 6, 9, and 24 h) were sampled at the same time by infiltrating bacteria at different times. The 20 infected leaves were harvested with forceps and immediately processed for nuclei extraction. For the mock condition, water-infiltrated leaves were harvested after 9 h.
Contributor(s) Nobori T, Ecker JR
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Submission date Mar 07, 2023
Last update date Nov 19, 2023
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL26208 Illumina NovaSeq 6000 (Arabidopsis thaliana)
Samples (30)
GSM7084718 AvrRpt2, 4h, RNA
GSM7084725 AvrRpt2, 4h, ATAC
GSM7084729 AvrRpt2, 6h, RNA
BioProject PRJNA941845
SRA SRP425955

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Supplementary file Size Download File type/resource
GSE226826_AvrRpm1_24h_peak.rds.gz 105.7 Mb (ftp)(http) RDS
GSE226826_AvrRpm1_4h_peak.rds.gz 91.0 Mb (ftp)(http) RDS
GSE226826_AvrRpm1_6h_peak.rds.gz 87.0 Mb (ftp)(http) RDS
GSE226826_AvrRpm1_9h_peak.rds.gz 185.4 Mb (ftp)(http) RDS
GSE226826_AvrRpt2_24h_peak.rds.gz 42.5 Mb (ftp)(http) RDS
GSE226826_AvrRpt2_4h_peak.rds.gz 92.2 Mb (ftp)(http) RDS
GSE226826_AvrRpt2_6h_peak.rds.gz 72.6 Mb (ftp)(http) RDS
GSE226826_AvrRpt2_9h_peak.rds.gz 60.6 Mb (ftp)(http) RDS
GSE226826_DC3000_24h_peak.rds.gz 92.0 Mb (ftp)(http) RDS
GSE226826_DC3000_4h_peak.rds.gz 113.1 Mb (ftp)(http) RDS
GSE226826_DC3000_6h_peak.rds.gz 157.7 Mb (ftp)(http) RDS
GSE226826_DC3000_9h_peak.rds.gz 116.4 Mb (ftp)(http) RDS
GSE226826_combined_filtered.rds.gz 5.2 Gb (ftp)(http) RDS
GSE226826_mock_peak.rds.gz 155.8 Mb (ftp)(http) RDS
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