Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics
Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step towards engineering improved drought resilience. The molecular responses to drought are however very complex as they depend on multiple factors including the severity of drought, the profiled organ, its developmental stage and even the cell types therein. As such, deciphering the transcriptional responses to drought is specifically challenging.In the study associated with this data submission, we investigated tissue-specific responses to mild drought in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq, deposited under another id, GSE273033). To preserve transcriptional integrity during cell isolation, we fixed the RNA prior to cell isolation using the transcription inhibitor actinomycin D, demonstrating the benefits of fixation for studying mild stress responses at single-cell level. The transcriptome data deposited here corresponds to the bulk RNA-sequencing experiments described in this study. The samples presented here are undigested leaves, leaves digested by cell wall degradation without fixation, and leaves digested by cell wall degradation with RNA fixation. All sample types were collected from plants growing under well-watered and mild drought conditions. Overall design: Arabidopsis Col-0 was grown either under well-watered conditions or exposed to mild drought. Per condition and per biological replicate, third true leaves were collected as "Undigested leaf" samples. They were harvested in 3 biological replicates. Third true leaves were also collected for tissue digestion, either without ("digested") or with RNA fixation("fixed, digested"). The obtained cells were subsequently processed for single-cell RNA sequencing (data deposited separately, GSE273033) or collected for bulk RNA sequencing (this deposition). These samples were harvested in two biological replicates.