Drought Recovery in Plants Triggers a Cell-State Specific Immune Activation
Cite
Illouz-Eliaz, N., Yu, J., Swift, J., Lande, K., Jow, B., Tuang, Z.K., Lee, T., Yaaran, A., Castanon, R.G., Nery, J.R. and Nobori, T., 2025. Drought recovery in plants triggers a cell-state-specific immune activation. Nat Commun 16, 8095 (2025). https://doi.org/10.1038/s41467-025-63467-2
Abstract
All organisms experience stress as an inevitable part of life, from single-celled microorganisms to complex multicellular beings. The ability to recover from stress is a fundamental trait that determines the overall resilience of an organism, yet stress recovery is understudied. To investigate how plants recover from drought, we examine a fine-scale time series of RNA sequencing starting 15 min after rehydration following moderate drought. We reveal that drought recovery is a rapid process involving the activation of thousands of recovery-specific genes. To capture these rapid recovery responses in different Arabidopsis thaliana (A. thaliana) leaf cell types, we perform a single-nucleus transcriptome analysis at the onset of drought recovery, identifying a cell type-specific transcriptional state developing independently across cell types. To further validate the cell-type specific transcriptional changes observed during drought recovery, we employ spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH), revealing anatomical localization of recovery-induced gene expression programs across Arabidopsis leaf tissues. Furthermore, we reveal a recovery-induced activation of the immune system that occurs autonomously, and which enhances pathogen resistance in vivo in A. thaliana, wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Since rehydration promotes microbial proliferation and thereby increases the risk of infection, the activation of drought recovery-induced immunity may be crucial for plant survival in natural environments. These findings indicate that drought recovery coincides with a preventive defense response, unraveling the complex regulatory mechanisms that facilitate stress recovery in different plant cell types.
Datasets
1. Integrated single-nucleus RNA-seq dataset of drought and recovery
ExploreSample ID
Treatment
Subject ID
Cell subtype
Cell type (Seurat clusters)
Cell type
Cell type (condition)
Cell subtype (condition)
GEO accession
Sample name
Tissue
Age
Genotype
Clusters (integrated_snn_res.8)
Seurat clusters
Assay
Treatment (short)
Disease
W15.226,746 cells
W15.122,697 cells
D0.220,440 cells
D0.119,494 cells
W0.218,824 cells
W0.115,876 cells
R15.110,681 cells
R15.29,736 cells
Well-watered84,143 cells
Drought 30% SWC39,934 cells
Drought + rehydration 15 mins20,417 cells
W15.226,746 cells
W15.122,697 cells
D0.220,440 cells
D0.119,494 cells
W0.218,824 cells
W0.115,876 cells
R15.110,681 cells
R15.29,736 cells
Mesophyll_120,842 cells
Mesophyll_216,347 cells
Mesophyll_313,880 cells
Mesophyll_412,145 cells
Mesophyll_511,803 cells
Epidermal_111,606 cells
Immune active8,152 cells
Mesophyll_66,460 cells
Guard_15,624 cells
Mesophyll_73,977 cells
Defense state3,877 cells
Vascular_13,540 cells
Vascular_23,445 cells
Epidermal_22,658 cells
Phloem companion2,489 cells
Stress responsive2,215 cells
Phloem Parenchyma2,049 cells
Sieve element_responsive2,021 cells
Dividing_12,014 cells
Guard_21,796 cells
Dividing_21,668 cells
Epidermal_31,597 cells
Metabolic stress state1,347 cells
Hydathode1,189 cells
Trichome900 cells
Myrosin484 cells
Sugar metabolic state369 cells
0: Mesophyll_120,842 cells
1: Mesophyll_216,347 cells
2: Mesophyll_313,880 cells
3: Mesophyll_412,145 cells
4: Mesophyll_511,803 cells
5: Epidermal_111,606 cells
6: Immune active8,152 cells
7: Mesophyll_66,460 cells
8: Guard_15,624 cells
9: Mesophyll_73,977 cells
10: Defense state3,877 cells
11: Vascular_13,540 cells
12: Vascular_23,445 cells
13: Epidermal_22,658 cells
14: Phloem companion2,489 cells
15: Stress responsive2,215 cells
16: Phloem Parenchyma2,049 cells
17: Sieve element_responsive2,021 cells
18: Dividing_12,014 cells
19: Guard_21,796 cells
20: Dividing_21,668 cells
21: Epidermal_31,597 cells
22: Metabolic stress state1,347 cells
23: Hydathode1,189 cells
24: Trichome900 cells
25: Myrosin484 cells
26: Sugar metabolic state369 cells
Mesophyll85,454 cells
Epidermal15,861 cells
Immune active8,152 cells
Guard7,420 cells
Vascular6,985 cells
Defense state3,877 cells
Dividing3,682 cells
Phloem companion2,489 cells
Stress responsive2,215 cells
Phloem Parenchyma2,049 cells
Sieve element_responsive2,021 cells
Metabolic stress state1,347 cells
Hydathode1,189 cells
Trichome900 cells
Myrosin484 cells
Sugar metabolic state369 cells
W15_Mesophyll31,671 cells
W0_Mesophyll23,473 cells
D0_Mesophyll21,703 cells
R15_Mesophyll8,607 cells
W15_Epidermal5,282 cells
D0_Epidermal4,610 cells
R15_Immune active4,306 cells
W0_Epidermal3,610 cells
W15_Immune active2,474 cells
R15_Epidermal2,359 cells
W15_Vascular2,347 cells
D0_Guard2,322 cells
W15_Guard2,235 cells
D0_Vascular2,034 cells
D0_Defense state2,034 cells
W0_Guard1,804 cells
W0_Vascular1,659 cells
W15_Dividing1,347 cells
W0_Dividing1,256 cells
D0_Metabolic stress state1,120 cells
R15_Guard1,059 cells
D0_Stress responsive1,049 cells
D0_Phloem companion1,002 cells
R15_Vascular945 cells
D0_Immune active943 cells
W15_Phloem Parenchyma887 cells
D0_Dividing844 cells
R15_Defense state803 cells
D0_Sieve element_responsive705 cells
W15_Defense state672 cells
R15_Sieve element_responsive624 cells
W15_Phloem companion575 cells
D0_Phloem Parenchyma551 cells
W15_Hydathode550 cells
W0_Phloem companion498 cells
W15_Stress responsive487 cells
W15_Sieve element_responsive457 cells
W0_Immune active429 cells
R15_Phloem companion414 cells
D0_Hydathode410 cells
W0_Phloem Parenchyma408 cells
W0_Stress responsive384 cells
W0_Defense state368 cells
D0_Trichome356 cells
R15_Stress responsive295 cells
W0_Trichome258 cells
W0_Sieve element_responsive235 cells
R15_Dividing235 cells
R15_Phloem Parenchyma203 cells
R15_Hydathode194 cells
W15_Myrosin165 cells
W15_Trichome149 cells
R15_Metabolic stress state141 cells
R15_Trichome137 cells
W0_Myrosin135 cells
D0_Myrosin133 cells
D0_Sugar metabolic state118 cells
W0_Sugar metabolic state106 cells
W15_Sugar metabolic state101 cells
R15_Myrosin51 cells
W15_Metabolic stress state44 cells
R15_Sugar metabolic state44 cells
W0_Metabolic stress state42 cells
W0_Hydathode35 cells
W15_Mesophyll_112,565 cells
W15_Mesophyll_25,645 cells
W0_Mesophyll_15,530 cells
W0_Mesophyll_34,722 cells
D0_Mesophyll_24,652 cells
W0_Mesophyll_24,530 cells
R15_Immune active4,306 cells
W15_Mesophyll_34,177 cells
W15_Epidermal_14,025 cells
D0_Mesophyll_53,950 cells
D0_Mesophyll_43,852 cells
W15_Mesophyll_53,772 cells
W0_Mesophyll_43,730 cells
D0_Mesophyll_33,339 cells
D0_Epidermal_13,314 cells
W15_Mesophyll_43,052 cells
D0_Mesophyll_62,757 cells
W0_Mesophyll_52,513 cells
W15_Immune active2,474 cells
W0_Epidermal_12,410 cells
D0_Defense state2,034 cells
R15_Epidermal_11,857 cells
D0_Mesophyll_11,857 cells
W15_Guard_11,828 cells
W15_Mesophyll_61,797 cells
D0_Guard_11,661 cells
R15_Mesophyll_31,642 cells
R15_Mesophyll_51,568 cells
R15_Mesophyll_21,520 cells
R15_Mesophyll_41,511 cells
W0_Mesophyll_71,482 cells
W0_Guard_11,379 cells
D0_Mesophyll_71,296 cells
W15_Vascular_21,201 cells
W15_Vascular_11,146 cells
D0_Metabolic stress state1,120 cells
D0_Stress responsive1,049 cells
D0_Vascular_11,048 cells
D0_Phloem companion1,002 cells
D0_Vascular_2986 cells
W0_Mesophyll_6966 cells
D0_Immune active943 cells
R15_Mesophyll_6940 cells
R15_Mesophyll_1890 cells
W15_Phloem Parenchyma887 cells
W0_Vascular_1841 cells
W0_Epidermal_2820 cells
W0_Vascular_2818 cells
W15_Epidermal_2816 cells
R15_Defense state803 cells
R15_Guard_1756 cells
D0_Epidermal_2751 cells
W0_Dividing_1735 cells
W15_Dividing_1732 cells
D0_Sieve element_responsive705 cells
W15_Defense state672 cells
W15_Mesophyll_7663 cells
D0_Guard_2661 cells
R15_Sieve element_responsive624 cells
W15_Dividing_2615 cells
W15_Phloem companion575 cells
D0_Phloem Parenchyma551 cells
W15_Hydathode550 cells
D0_Epidermal_3545 cells
R15_Mesophyll_7536 cells
W0_Dividing_2521 cells
R15_Vascular_1505 cells
W0_Phloem companion498 cells
W15_Stress responsive487 cells
W15_Sieve element_responsive457 cells
W15_Epidermal_3441 cells
R15_Vascular_2440 cells
W0_Immune active429 cells
W0_Guard_2425 cells
D0_Dividing_2425 cells
D0_Dividing_1419 cells
R15_Phloem companion414 cells
D0_Hydathode410 cells
W0_Phloem Parenchyma408 cells
W15_Guard_2407 cells
W0_Stress responsive384 cells
W0_Epidermal_3380 cells
W0_Defense state368 cells
D0_Trichome356 cells
R15_Guard_2303 cells
R15_Stress responsive295 cells
R15_Epidermal_2271 cells
W0_Trichome258 cells
W0_Sieve element_responsive235 cells
R15_Epidermal_3231 cells
R15_Phloem Parenchyma203 cells
R15_Hydathode194 cells
W15_Myrosin165 cells
W15_Trichome149 cells
R15_Metabolic stress state141 cells
R15_Trichome137 cells
W0_Myrosin135 cells
D0_Myrosin133 cells
R15_Dividing_1128 cells
D0_Sugar metabolic state118 cells
R15_Dividing_2107 cells
W0_Sugar metabolic state106 cells
W15_Sugar metabolic state101 cells
R15_Myrosin51 cells
W15_Metabolic stress state44 cells
R15_Sugar metabolic state44 cells
W0_Metabolic stress state42 cells
W0_Hydathode35 cells
GSM822317026,746 cells
GSM822316922,697 cells
GSM822316820,440 cells
GSM822316719,494 cells
GSM822316618,824 cells
GSM822316515,876 cells
GSM822317110,681 cells
GSM82231729,736 cells
well-watered_verm_time15_rep2, snRNAseq26,746 cells
well-watered_verm_time15_rep1, snRNAseq22,697 cells
drought_verm_time0_rep2, snRNAseq20,440 cells
drought_verm_time0_rep1, snRNAseq19,494 cells
well-watered_verm_time0_rep2, snRNAseq18,824 cells
well-watered_verm_time0_rep1, snRNAseq15,876 cells
recovery_verm_time15_rep1, snRNAseq10,681 cells
recovery_verm_time15_rep2, snRNAseq9,736 cells
Whole rosette144,494 cells
40-day-old144,494 cells
Col - 0144,494 cells
Cluster 020,842 cells
Cluster 116,347 cells
Cluster 213,880 cells
Cluster 312,145 cells
Cluster 411,803 cells
Cluster 511,606 cells
Cluster 68,152 cells
Cluster 76,460 cells
Cluster 85,624 cells
Cluster 93,977 cells
Cluster 103,877 cells
Cluster 113,540 cells
Cluster 123,445 cells
Cluster 132,658 cells
Cluster 142,489 cells
Cluster 152,215 cells
Cluster 162,049 cells
Cluster 172,021 cells
Cluster 182,014 cells
Cluster 191,796 cells
Cluster 201,668 cells
Cluster 211,597 cells
Cluster 221,347 cells
Cluster 231,189 cells
Cluster 24900 cells
Cluster 25484 cells
Cluster 26369 cells
Cluster 020,842 cells
Cluster 116,347 cells
Cluster 213,880 cells
Cluster 312,145 cells
Cluster 411,803 cells
Cluster 511,606 cells
Cluster 68,152 cells
Cluster 76,460 cells
Cluster 85,624 cells
Cluster 93,977 cells
Cluster 103,877 cells
Cluster 113,540 cells
Cluster 123,445 cells
Cluster 132,658 cells
Cluster 142,489 cells
Cluster 152,215 cells
Cluster 162,049 cells
Cluster 172,021 cells
Cluster 182,014 cells
Cluster 191,796 cells
Cluster 201,668 cells
Cluster 211,597 cells
Cluster 221,347 cells
Cluster 231,189 cells
Cluster 24900 cells
Cluster 25484 cells
Cluster 26369 cells
10X Genomics 3’, Gene Expression HT-v3.1, single-nucleus144,494 cells
W1549,443 cells
D039,934 cells
W034,700 cells
R1520,417 cells
normal144,494 cells
2. Single-nucleus RNA-seq of plants during dehydration
ExploreDay
Cell type
Group
Sample name
Tissue
Age
Genotype
Treatment
Assay
Disease
Sample ID
Day_56,184 cells
Day_14,812 cells
Day_22,866 cells
Day_32,687 cells
Day_41,790 cells
Day_01,202 cells
Mesophyll_33,098 cells
Mesophyll_12,820 cells
Mesophyll_22,786 cells
Epidermal_12,581 cells
Mesophyll_41,660 cells
Guard961 cells
Epidermal_2896 cells
Hydathode878 cells
Mesophyll_5718 cells
Phloem companion669 cells
Mesophyll_7661 cells
Unknown_1539 cells
Mesophyll_6445 cells
Dividing423 cells
Vascular224 cells
Unknown_2102 cells
Myrosin80 cells
0_Day_51,100 cells
3_Day_5953 cells
2_Day_1903 cells
1_Day_5831 cells
1_Day_1774 cells
2_Day_5681 cells
3_Day_1618 cells
4_Day_5610 cells
2_Day_3607 cells
0_Day_1568 cells
2_Day_2497 cells
0_Day_2405 cells
1_Day_3367 cells
1_Day_2367 cells
0_Day_3366 cells
4_Day_1342 cells
6_Day_5313 cells
1_Day_4311 cells
3_Day_3309 cells
3_Day_2305 cells
13_Day_5275 cells
5_Day_5269 cells
2_Day_0266 cells
0_Day_4259 cells
3_Day_4251 cells
5_Day_1247 cells
4_Day_2240 cells
4_Day_3234 cells
8_Day_5225 cells
7_Day_5211 cells
6_Day_1210 cells
10_Day_1206 cells
6_Day_2205 cells
7_Day_1184 cells
9_Day_1178 cells
8_Day_1175 cells
9_Day_5175 cells
7_Day_2167 cells
10_Day_5159 cells
11_Day_1156 cells
4_Day_4151 cells
7_Day_3145 cells
3_Day_0145 cells
2_Day_4144 cells
11_Day_5142 cells
10_Day_2138 cells
1_Day_0136 cells
0_Day_0122 cells
12_Day_1121 cells
12_Day_5113 cells
5_Day_3113 cells
6_Day_3112 cells
9_Day_2108 cells
7_Day_0101 cells
5_Day_497 cells
5_Day_294 cells
10_Day_394 cells
7_Day_488 cells
6_Day_485 cells
11_Day_483 cells
4_Day_083 cells
8_Day_282 cells
9_Day_379 cells
9_Day_478 cells
8_Day_477 cells
10_Day_076 cells
8_Day_372 cells
13_Day_268 cells
11_Day_268 cells
14_Day_166 cells
14_Day_561 cells
12_Day_258 cells
5_Day_058 cells
11_Day_356 cells
12_Day_355 cells
12_Day_451 cells
10_Day_445 cells
9_Day_043 cells
15_Day_539 cells
8_Day_038 cells
6_Day_036 cells
11_Day_034 cells
14_Day_233 cells
13_Day_132 cells
13_Day_432 cells
13_Day_332 cells
16_Day_527 cells
12_Day_025 cells
14_Day_425 cells
14_Day_320 cells
15_Day_219 cells
14_Day_019 cells
16_Day_118 cells
16_Day_315 cells
15_Day_114 cells
16_Day_212 cells
15_Day_311 cells
15_Day_011 cells
15_Day_48 cells
13_Day_06 cells
16_Day_45 cells
16_Day_03 cells
timecourse_drought_day5, snRNAseq6,184 cells
timecourse_drought_day1, snRNAseq4,812 cells
timecourse_drought_day2, snRNAseq2,866 cells
timecourse_drought_day3, snRNAseq2,687 cells
timecourse_drought_day4, snRNAseq1,790 cells
timecourse_drought_day0, snRNAseq1,202 cells
Whole rosette19,541 cells
34-day-old6,184 cells
30-day-old4,812 cells
31-day-old2,866 cells
32-day-old2,687 cells
33-day-old1,790 cells
29-day-old1,202 cells
Col - 019,541 cells
Drought Day 5 (37% SWC)6,184 cells
Drought Day 1 (86% SWC)4,812 cells
Drought Day 2 (73% SWC)2,866 cells
Drought Day 3 (62% SWC)2,687 cells
Drought Day 4 (49% SWC)1,790 cells
Drought Day 0 (100% SWC)1,202 cells
10X Genomics 3’, Gene Expression HT-v3.1, single-nucleus19,541 cells
normal19,541 cells
timecourse_drought_day56,184 cells
timecourse_drought_day14,812 cells
timecourse_drought_day22,866 cells
timecourse_drought_day32,687 cells
timecourse_drought_day41,790 cells
timecourse_drought_day01,202 cells
3. Bulk RNA-seq time course of drought recovering plants - Run 1
ExploreLeiden clustering
Sample ID
Sample name
GEO accession
Tissue
Cell line
Genotype
Treatment
Treatment group
Timepoint
Assay
Age
Disease
Treatment + Timepoint
Treatment group - Timepoint
Cluster 325 cells
Cluster 221 cells
Cluster 18 cells
Bulk1_ww90-31 cells
Bulk1_ww90-21 cells
Bulk1_ww90-11 cells
Bulk1_ww60-31 cells
Bulk1_ww60-21 cells
Bulk1_ww60-11 cells
Bulk1_ww4h-31 cells
Bulk1_ww4h-21 cells
Bulk1_ww4h-11 cells
Bulk1_ww30-31 cells
Bulk1_ww30-21 cells
Bulk1_ww30-11 cells
Bulk1_ww15-31 cells
Bulk1_ww15-21 cells
Bulk1_ww15-11 cells
Bulk1_ww120-31 cells
Bulk1_ww120-21 cells
Bulk1_ww120-11 cells
Bulk1_ww-0-31 cells
Bulk1_ww-0-21 cells
Bulk1_ww-0-11 cells
Bulk1_w6h-31 cells
Bulk1_w6h-21 cells
Bulk1_w6h-11 cells
Bulk1_W48h-31 cells
Bulk1_W48h-21 cells
Bulk1_W48h-11 cells
Bulk1_R90-31 cells
Bulk1_R90-21 cells
Bulk1_R90-11 cells
Bulk1_R6h-31 cells
Bulk1_R6h-21 cells
Bulk1_R6h-11 cells
Bulk1_R60-31 cells
Bulk1_R60-21 cells
Bulk1_R60-11 cells
Bulk1_R4h-31 cells
Bulk1_R4h-21 cells
Bulk1_R4h-11 cells
Bulk1_R15-31 cells
Bulk1_R15-21 cells
Bulk1_R15-11 cells
Bulk1_R120-31 cells
Bulk1_R120-21 cells
Bulk1_R120-11 cells
Bulk1_R-48h-31 cells
Bulk1_R-48h-21 cells
Bulk1_R-48h-11 cells
Bulk1_R-30-31 cells
Bulk1_R-30-21 cells
Bulk1_R-30-11 cells
Bulk1_D30-31 cells
Bulk1_D30-21 cells
Bulk1_D30-11 cells
Bulk1_Well-watered time 90 mins, rep31 cells
Bulk1_Well-watered time 90 mins, rep21 cells
Bulk1_Well-watered time 90 mins, rep11 cells
Bulk1_Well-watered time 60 mins, rep31 cells
Bulk1_Well-watered time 60 mins, rep21 cells
Bulk1_Well-watered time 60 mins, rep11 cells
Bulk1_Well-watered time 6 hours, rep31 cells
Bulk1_Well-watered time 6 hours, rep21 cells
Bulk1_Well-watered time 6 hours, rep11 cells
Bulk1_Well-watered time 4 hours, rep31 cells
Bulk1_Well-watered time 4 hours, rep21 cells
Bulk1_Well-watered time 4 hours, rep11 cells
Bulk1_Well-watered time 30 mins, rep31 cells
Bulk1_Well-watered time 30 mins, rep21 cells
Bulk1_Well-watered time 30 mins, rep11 cells
Bulk1_Well-watered time 15 mins, rep31 cells
Bulk1_Well-watered time 15 mins, rep21 cells
Bulk1_Well-watered time 15 mins, rep11 cells
Bulk1_Well-watered time 120 mins, rep31 cells
Bulk1_Well-watered time 120 mins, rep21 cells
Bulk1_Well-watered time 120 mins, rep11 cells
Bulk1_Well-watered time 0, rep31 cells
Bulk1_Well-watered time 0, rep21 cells
Bulk1_Well-watered time 0, rep11 cells
Bulk1_Drought 30% SWC time 0, rep31 cells
Bulk1_Drought 30% SWC time 0, rep21 cells
Bulk1_Drought 30% SWC time 0, rep11 cells
Bulk1_Drought 30% SWC + Recovery 90 mins, rep31 cells
Bulk1_Drought 30% SWC + Recovery 90 mins, rep21 cells
Bulk1_Drought 30% SWC + Recovery 90 mins, rep11 cells
Bulk1_Drought 30% SWC + Recovery 60 mins, rep31 cells
Bulk1_Drought 30% SWC + Recovery 60 mins, rep21 cells
Bulk1_Drought 30% SWC + Recovery 60 mins, rep11 cells
Bulk1_Drought 30% SWC + Recovery 6 hours, rep31 cells
Bulk1_Drought 30% SWC + Recovery 6 hours, rep21 cells
Bulk1_Drought 30% SWC + Recovery 6 hours, rep11 cells
Bulk1_Drought 30% SWC + Recovery 48 hours, rep31 cells
Bulk1_Drought 30% SWC + Recovery 48 hours, rep21 cells
Bulk1_Drought 30% SWC + Recovery 48 hours, rep11 cells
Bulk1_Drought 30% SWC + Recovery 4 hours, rep31 cells
Bulk1_Drought 30% SWC + Recovery 4 hours, rep21 cells
Bulk1_Drought 30% SWC + Recovery 4 hours, rep11 cells
Bulk1_Drought 30% SWC + Recovery 30 mins, rep31 cells
Bulk1_Drought 30% SWC + Recovery 30 mins, rep21 cells
Bulk1_Drought 30% SWC + Recovery 30 mins, rep11 cells
Bulk1_Drought 30% SWC + Recovery 15 mins, rep31 cells
Bulk1_Drought 30% SWC + Recovery 15 mins, rep21 cells
Bulk1_Drought 30% SWC + Recovery 15 mins , rep11 cells
Bulk1_Drought 30% SWC + Recovery 120 mins, rep31 cells
Bulk1_Drought 30% SWC + Recovery 120 mins, rep21 cells
Bulk1_Drought 30% SWC + Recovery 120 mins, rep11 cells
Bulk1Well-watered time 48 hours, rep31 cells
Bulk1Well-watered time 48 hours, rep21 cells
Bulk1Well-watered time 48 hours, rep11 cells
GSM67977191 cells
GSM67977181 cells
GSM67977171 cells
GSM67977161 cells
GSM67977151 cells
GSM67977141 cells
GSM67977131 cells
GSM67977121 cells
GSM67977111 cells
GSM67977101 cells
GSM67977091 cells
GSM67977081 cells
GSM67977071 cells
GSM67977061 cells
GSM67977051 cells
GSM67977041 cells
GSM67977031 cells
GSM67977021 cells
GSM67977011 cells
GSM67977001 cells
GSM67976991 cells
GSM67976981 cells
GSM67976971 cells
GSM67976961 cells
GSM67976951 cells
GSM67976941 cells
GSM67976931 cells
GSM67976921 cells
GSM67976911 cells
GSM67976901 cells
GSM67976891 cells
GSM67976881 cells
GSM67976871 cells
GSM67976861 cells
GSM67976851 cells
GSM67976841 cells
GSM67976831 cells
GSM67976821 cells
GSM67976811 cells
GSM67976801 cells
GSM67976791 cells
GSM67976781 cells
GSM67976771 cells
GSM67976761 cells
GSM67976751 cells
GSM67976741 cells
GSM67976731 cells
GSM67976721 cells
GSM67976711 cells
GSM67976701 cells
GSM67976691 cells
GSM67976681 cells
GSM67976671 cells
GSM67976661 cells
Whole Rosette54 cells
Vermaculite54 cells
Col-054 cells
Well-watered time 90 mins3 cells
Well-watered time 60 mins3 cells
Well-watered time 6 hours3 cells
Well-watered time 48 hours3 cells
Well-watered time 4 hours3 cells
Well-watered time 30 mins3 cells
Well-watered time 15 mins3 cells
Well-watered time 120 mins3 cells
Well-watered time 03 cells
Drought 30% SWC + Recovery 90 mins3 cells
Drought 30% SWC + Recovery 60 mins3 cells
Drought 30% SWC + Recovery 6 hours3 cells
Drought 30% SWC + Recovery 48 hours3 cells
Drought 30% SWC + Recovery 4 hours3 cells
Drought 30% SWC + Recovery 30 mins3 cells
Drought 30% SWC + Recovery 15 mins3 cells
Drought 30% SWC + Recovery 120 mins3 cells
Drought 30% SWC (time 0)3 cells
Well-watered27 cells
Drought 30% SWC + Recovery27 cells
T8 - 48 hours6 cells
T7 - 6 hours6 cells
T6 - 4 hours6 cells
T5 - 20 mins6 cells
T4 - 90 mins6 cells
T3 - 60 mins6 cells
T2 - 30 mins6 cells
T1 - 15 mins6 cells
T0 - time 06 cells
Illumina TruSeq, RNeasy Plant Mini Kits54 cells
30+ days54 cells
normal54 cells
Well-watered time 90 mins - T4 - 90 mins3 cells
Well-watered time 60 mins - T3 - 60 mins3 cells
Well-watered time 6 hours - T7 - 6 hours3 cells
Well-watered time 48 hours - T8 - 48 hours3 cells
Well-watered time 4 hours - T6 - 4 hours3 cells
Well-watered time 30 mins - T2 - 30 mins3 cells
Well-watered time 15 mins - T1 - 15 mins3 cells
Well-watered time 120 mins - T5 - 20 mins3 cells
Well-watered time 0 - T0 - time 03 cells
Drought 30% SWC + Recovery 90 mins - T4 - 90 mins3 cells
Drought 30% SWC + Recovery 60 mins - T3 - 60 mins3 cells
Drought 30% SWC + Recovery 6 hours - T7 - 6 hours3 cells
Drought 30% SWC + Recovery 48 hours - T8 - 48 hours3 cells
Drought 30% SWC + Recovery 4 hours - T6 - 4 hours3 cells
Drought 30% SWC + Recovery 30 mins - T2 - 30 mins3 cells
Drought 30% SWC + Recovery 15 mins - T1 - 15 mins3 cells
Drought 30% SWC + Recovery 120 mins - T5 - 20 mins3 cells
Drought 30% SWC (time 0) - T0 - time 03 cells
Well-watered - T8 - 48 hours3 cells
Well-watered - T7 - 6 hours3 cells
Well-watered - T6 - 4 hours3 cells
Well-watered - T5 - 20 mins3 cells
Well-watered - T4 - 90 mins3 cells
Well-watered - T3 - 60 mins3 cells
Well-watered - T2 - 30 mins3 cells
Well-watered - T1 - 15 mins3 cells
Well-watered - T0 - time 03 cells
Drought 30% SWC + Recovery - T8 - 48 hours3 cells
Drought 30% SWC + Recovery - T7 - 6 hours3 cells
Drought 30% SWC + Recovery - T6 - 4 hours3 cells
Drought 30% SWC + Recovery - T5 - 20 mins3 cells
Drought 30% SWC + Recovery - T4 - 90 mins3 cells
Drought 30% SWC + Recovery - T3 - 60 mins3 cells
Drought 30% SWC + Recovery - T2 - 30 mins3 cells
Drought 30% SWC + Recovery - T1 - 15 mins3 cells
Drought 30% SWC + Recovery - T0 - time 03 cells
Well-watered - T8 - 48 hours3 cells
Well-watered - T7 - 6 hours3 cells
Well-watered - T6 - 4 hours3 cells
Well-watered - T5 - 20 mins3 cells
Well-watered - T4 - 90 mins3 cells
Well-watered - T3 - 60 mins3 cells
Well-watered - T2 - 30 mins3 cells
Well-watered - T1 - 15 mins3 cells
Well-watered - T0 - time 03 cells
Drought 30% SWC + Recovery - T8 - 48 hours3 cells
Drought 30% SWC + Recovery - T7 - 6 hours3 cells
Drought 30% SWC + Recovery - T6 - 4 hours3 cells
Drought 30% SWC + Recovery - T5 - 20 mins3 cells
Drought 30% SWC + Recovery - T4 - 90 mins3 cells
Drought 30% SWC + Recovery - T3 - 60 mins3 cells
Drought 30% SWC + Recovery - T2 - 30 mins3 cells
Drought 30% SWC + Recovery - T1 - 15 mins3 cells
Drought 30% SWC + Recovery - T0 - time 03 cells
4. Bulk RNA-seq time course of drought recovering plants - Run 2
ExploreLeiden clustering
Sample ID
Sample name
GEO accession
Tissue
Cell line
Genotype
Treatment
Age
Assay
Disease
Cluster 17 cells
Cluster 26 cells
Cluster 36 cells
Cluster 45 cells
Bulk2_W_60-31 cells
Bulk2_W_60-21 cells
Bulk2_W_60-11 cells
Bulk2_W_120-31 cells
Bulk2_W_120-21 cells
Bulk2_W_120-11 cells
Bulk2_W_0-31 cells
Bulk2_W_0-21 cells
Bulk2_W_0-11 cells
Bulk2_R_50%_60-31 cells
Bulk2_R_50%_60-21 cells
Bulk2_R_50%_60-11 cells
Bulk2_R_50%_30-31 cells
Bulk2_R_50%_30-21 cells
Bulk2_R_50%_30-11 cells
Bulk2_R_50%_15-31 cells
Bulk2_R_50%_15-21 cells
Bulk2_R_50%_15-11 cells
Bulk2_R_50%_120-31 cells
Bulk2_R_50%_120-21 cells
Bulk2_R_50%_120-11 cells
Bulk2_D_50%-31 cells
Bulk2_D_50%-21 cells
Bulk2_D_50%-11 cells
Bulk2_recovery_ time 120, rep31 cells
Bulk2_recovery_ time 120, rep21 cells
Bulk2_recovery_ time 120, rep11 cells
Bulk2_Well-watered time 60 mins, rep31 cells
Bulk2_Well-watered time 60 mins, rep21 cells
Bulk2_Well-watered time 60 mins, rep11 cells
Bulk2_Well-watered time 120 mins, rep31 cells
Bulk2_Well-watered time 120 mins, rep21 cells
Bulk2_Well-watered time 120 mins, rep11 cells
Bulk2_Well-watered time 0, rep31 cells
Bulk2_Well-watered time 0, rep21 cells
Bulk2_Well-watered time 0, rep11 cells
Bulk2_Stress_50%, rep31 cells
Bulk2_Stress_50%, rep21 cells
Bulk2_Stress_50%, rep11 cells
Bulk2_Recovery_time 60, rep31 cells
Bulk2_Recovery_time 60, rep21 cells
Bulk2_Recovery_time 60, rep11 cells
Bulk2_Recovery_time 30, rep31 cells
Bulk2_Recovery_time 30, rep21 cells
Bulk2_Recovery_time 30, rep11 cells
Bulk2_Recovery_time 15, rep31 cells
Bulk2_Recovery_time 15, rep21 cells
Bulk2_Recovery_time 15, rep11 cells
GSM67977431 cells
GSM67977421 cells
GSM67977411 cells
GSM67977401 cells
GSM67977391 cells
GSM67977381 cells
GSM67977371 cells
GSM67977361 cells
GSM67977351 cells
GSM67977341 cells
GSM67977331 cells
GSM67977321 cells
GSM67977311 cells
GSM67977301 cells
GSM67977291 cells
GSM67977281 cells
GSM67977271 cells
GSM67977261 cells
GSM67977251 cells
GSM67977241 cells
GSM67977231 cells
GSM67977221 cells
GSM67977211 cells
GSM67977201 cells
Whole Rosette24 cells
LW Plates24 cells
Col-024 cells
recovery_ time 1203 cells
Well-watered time 60 mins3 cells
Well-watered time 120 mins3 cells
Well-watered time 03 cells
Stress_50%3 cells
Recovery_time 603 cells
Recovery_time 303 cells
Recovery_time 153 cells
30+ days24 cells
Illumina TruSeq, RNeasy Plant Mini Kits24 cells
normal24 cells
5. Bulk RNA-seq time course of drought recovering plants - Run 3
ExploreLeiden clustering
Sample ID
Sample name
GEO accession
Tissue
Cell line
Genotype
Treatment
Disease
Age
Assay
Cluster 218 cells
Cluster 118 cells
Bulk3_W_R30_31 cells
Bulk3_W_R30_21 cells
Bulk3_W_R30_11 cells
Bulk3_W_R15_31 cells
Bulk3_W_R15_21 cells
Bulk3_W_R15_11 cells
Bulk3_W_90-31 cells
Bulk3_W_90-21 cells
Bulk3_W_90-11 cells
Bulk3_W_60-31 cells
Bulk3_W_60-21 cells
Bulk3_W_60-11 cells
Bulk3_W_120-31 cells
Bulk3_W_120-21 cells
Bulk3_W_120-11 cells
Bulk3_W_0-31 cells
Bulk3_W_0-21 cells
Bulk3_W_0-11 cells
Bulk3_R_25%_90-31 cells
Bulk3_R_25%_90-21 cells
Bulk3_R_25%_90-11 cells
Bulk3_R_25%_60-31 cells
Bulk3_R_25%_60-21 cells
Bulk3_R_25%_60-11 cells
Bulk3_R_25%_30-31 cells
Bulk3_R_25%_30-21 cells
Bulk3_R_25%_30-11 cells
Bulk3_R_25%_15-31 cells
Bulk3_R_25%_15-21 cells
Bulk3_R_25%_15-11 cells
Bulk3_R_25%_120-31 cells
Bulk3_R_25%_120-21 cells
Bulk3_R_25%_120-11 cells
Bulk3_D_25%-31 cells
Bulk3_D_25%-21 cells
Bulk3_D_25%-11 cells
Bulk3_well-watered time 90, rep31 cells
Bulk3_well-watered time 90, rep21 cells
Bulk3_well-watered time 90, rep11 cells
Bulk3_well-watered time 60, rep31 cells
Bulk3_well-watered time 60, rep21 cells
Bulk3_well-watered time 60, rep11 cells
Bulk3_well-watered time 30, rep31 cells
Bulk3_well-watered time 30, rep21 cells
Bulk3_well-watered time 30, rep11 cells
Bulk3_well-watered time 15, rep31 cells
Bulk3_well-watered time 15, rep21 cells
Bulk3_well-watered time 15, rep11 cells
Bulk3_well-watered time 120, rep31 cells
Bulk3_well-watered time 120, rep21 cells
Bulk3_well-watered time 120, rep11 cells
Bulk3_well-watered time 0, rep31 cells
Bulk3_well-watered time 0, rep21 cells
Bulk3_well-watered time 0, rep11 cells
Bulk3_Stress_25%, rep31 cells
Bulk3_Stress_25%, rep21 cells
Bulk3_Stress_25%, rep11 cells
Bulk3_Recovery_25% time 90, rep31 cells
Bulk3_Recovery_25% time 90, rep21 cells
Bulk3_Recovery_25% time 90, rep11 cells
Bulk3_Recovery_25% time 60, rep31 cells
Bulk3_Recovery_25% time 60, rep21 cells
Bulk3_Recovery_25% time 60, rep11 cells
Bulk3_Recovery_25% time 30, rep31 cells
Bulk3_Recovery_25% time 30, rep21 cells
Bulk3_Recovery_25% time 30, rep11 cells
Bulk3_Recovery_25% time 15, rep31 cells
Bulk3_Recovery_25% time 15, rep21 cells
Bulk3_Recovery_25% time 15, rep11 cells
Bulk3_Recovery_25% time 120, rep31 cells
Bulk3_Recovery_25% time 120, rep21 cells
Bulk3_Recovery_25% time 120, rep11 cells
GSM67977791 cells
GSM67977781 cells
GSM67977771 cells
GSM67977761 cells
GSM67977751 cells
GSM67977741 cells
GSM67977731 cells
GSM67977721 cells
GSM67977711 cells
GSM67977701 cells
GSM67977691 cells
GSM67977681 cells
GSM67977671 cells
GSM67977661 cells
GSM67977651 cells
GSM67977641 cells
GSM67977631 cells
GSM67977621 cells
GSM67977611 cells
GSM67977601 cells
GSM67977591 cells
GSM67977581 cells
GSM67977571 cells
GSM67977561 cells
GSM67977551 cells
GSM67977541 cells
GSM67977531 cells
GSM67977521 cells
GSM67977511 cells
GSM67977501 cells
GSM67977491 cells
GSM67977481 cells
GSM67977471 cells
GSM67977461 cells
GSM67977451 cells
GSM67977441 cells
Whole Rosette36 cells
LW Plates36 cells
Col-036 cells
well-watered time 903 cells
well-watered time 603 cells
well-watered time 303 cells
well-watered time 153 cells
well-watered time 1203 cells
well-watered time 03 cells
Stress_25%3 cells
Recovery_25% time 903 cells
Recovery_25% time 603 cells
Recovery_25% time 303 cells
Recovery_25% time 153 cells
Recovery_25% time 1203 cells
normal36 cells
30+ days36 cells
Illumina TruSeq, RNeasy Plant Mini Kits36 cells
6. Bulk RNA-seq profilling of Col and camta1 mutants samples
ExploreLeiden clustering
Sample ID
Sample name
GEO accession
Tissue
Genotype
Treatment
Disease
Age
Assay
Cluster 210 cells
Cluster 18 cells
Cluster 37 cells
Cluster 43 cells
210915_Ath_40do_camta1_W_41 cells
210915_Ath_40do_camta1_W_31 cells
210915_Ath_40do_camta1_W_21 cells
210915_Ath_40do_camta1_W_11 cells
210915_Ath_40do_camta1_W15_31 cells
210915_Ath_40do_camta1_W15_21 cells
210915_Ath_40do_camta1_W15_11 cells
210915_Ath_40do_camta1_R15_31 cells
210915_Ath_40do_camta1_R15_21 cells
210915_Ath_40do_camta1_R15_11 cells
210915_Ath_40do_camta1_D_41 cells
210915_Ath_40do_camta1_D_31 cells
210915_Ath_40do_camta1_D_21 cells
210915_Ath_40do_camta1_D_11 cells
210915_Ath_40do_Col_W_41 cells
210915_Ath_40do_Col_W_31 cells
210915_Ath_40do_Col_W_21 cells
210915_Ath_40do_Col_W_11 cells
210915_Ath_40do_Col_W15_31 cells
210915_Ath_40do_Col_W15_21 cells
210915_Ath_40do_Col_W15_11 cells
210915_Ath_40do_Col_R15_31 cells
210915_Ath_40do_Col_R15_21 cells
210915_Ath_40do_Col_R15_11 cells
210915_Ath_40do_Col_D_41 cells
210915_Ath_40do_Col_D_31 cells
210915_Ath_40do_Col_D_21 cells
210915_Ath_40do_Col_D_11 cells
camta1 well-watered replicate 41 cells
camta1 well-watered replicate 31 cells
camta1 well-watered replicate 21 cells
camta1 well-watered replicate 11 cells
camta1 well-watered 15 minutes replicate 31 cells
camta1 well-watered 15 minutes replicate 21 cells
camta1 well-watered 15 minutes replicate 11 cells
camta1 stress recovery 15 minutes replicate 31 cells
camta1 stress recovery 15 minutes replicate 21 cells
camta1 stress recovery 15 minutes replicate 11 cells
camta1 moderate stress replicate 41 cells
camta1 moderate stress replicate 31 cells
camta1 moderate stress replicate 21 cells
camta1 moderate stress replicate 11 cells
Col well-watered replicate 41 cells
Col well-watered replicate 31 cells
Col well-watered replicate 21 cells
Col well-watered replicate 11 cells
Col well-watered 15 minutes replicate 31 cells
Col well-watered 15 minutes replicate 21 cells
Col well-watered 15 minutes replicate 11 cells
Col stress recovery 15 minutes replicate 31 cells
Col stress recovery 15 minutes replicate 21 cells
Col stress recovery 15 minutes replicate 11 cells
Col moderate stress replicate 41 cells
Col moderate stress replicate 31 cells
Col moderate stress replicate 21 cells
Col moderate stress replicate 11 cells
GSM87823171 cells
GSM87823161 cells
GSM87823151 cells
GSM87823141 cells
GSM87823131 cells
GSM87823121 cells
GSM87823111 cells
GSM87823101 cells
GSM87823091 cells
GSM87823081 cells
GSM87823071 cells
GSM87823061 cells
GSM87823051 cells
GSM87823041 cells
GSM87823031 cells
GSM87823021 cells
GSM87823011 cells
GSM87823001 cells
GSM87822991 cells
GSM87822981 cells
GSM87822971 cells
GSM87822961 cells
GSM87822951 cells
GSM87822941 cells
GSM87822931 cells
GSM87822921 cells
GSM87822911 cells
GSM87822901 cells
Leaves28 cells
camta1 (SALK_008187.38.30.x)14 cells
Col-0 (WT)14 cells
Well-watered (Control plates, with 100% water content)8 cells
Moderate osmotic stress (low-water plates, with 50% water content based on method describes in Gonzalez et al., 2023)8 cells
Well-watered (Control plates, with 100% water content, collected 15 minutes after transfer to new control plates with additional water)6 cells
Recovery from moderate osmotic stress (collected 15 minutes after trasfer to control plates)6 cells
normal28 cells
28+ days28 cells
Illumina TruSeq28 cells
7. Spatial transcriptomics of Arabidopsis leaf tissue under four water conditions
ExploreCell type
Sample ID
Treatment
GEO accession
Tissue
Disease
Assay
Leiden clustering
Leiden clustering (resolution=1)
Cell subtype
Mesophyll3,430 cells
Epidermal1,156 cells
Vascular108 cells
region R151,729 cells
region D01,543 cells
region W0764 cells
region W15658 cells
drought treated, rehydrated for 15 minutes1,729 cells
drought treated, time 0 (30% SWC)1,543 cells
well-watered, time 0 (1 hour after light turns on)764 cells
well-watered, 15 minutes658 cells
GSM91350191,729 cells
GSM91350181,543 cells
GSM9135020764 cells
GSM9135021658 cells
Leaves4,694 cells
normal4,694 cells
MERSCOPE4,694 cells
Cluster 11,931 cells
Cluster 21,437 cells
Cluster 31,326 cells
Cluster 41,097 cells
Cluster 1894 cells
Cluster 5581 cells
Cluster 8554 cells
Cluster 6390 cells
Cluster 3364 cells
Cluster 10308 cells
Cluster 7231 cells
Cluster 2155 cells
Cluster 9120 cells
Mesophyll_22,905 cells
Epidermal1,156 cells
Mesophyll_1525 cells
Vascular108 cells
Alias names
GSE220278, GSE220277, GSE220276, GSE289042, GSE303744