High-throughput single-cell RNA sequencing (scRNAseq) is widely used to study transcriptomes at single-cell resolution. In plants, this is challenging and most existing scRNAseq datasets do not indicate when samples were harvested. But it is known that the transcriptome changes depending on day / night cycles – the circadian clock. Differences are most pronounced between the end of the day (ED) and the end of the night (EN).

This recent PLAMORF publication fills this gap with scRNAseq studies on Arabidopsis root and above-ground tissues at defined times of the day. Gene expression of nearly 70,000 cells  was analysed at single-cell resolution to gain insights into spatial and circadian control of gene expression.

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Figure 1: Experimental overview with clustering and DEGs. A, Roots were harvested at the ED from 7-d-old plants approx. 1 cm below the hypocotyl (indicated by the black line); the above-ground tissue was harvested at the ED and EN from 5-week-old plants. For the single-cell samples, the tissue was harvested 75 min before the ED (or EN) time point and used for protoplast preparation. For the reference RNAseq libraries, the tissue was harvested 15 min before the ED (or EN) time point and shock frozen in liquid nitrogen. B, Hierarchical clustering of the sequenced scRNAseq (sc) and reference RNAseq (ref) libraries using Pearson’s correlation coefficient (r) as distance measure. C, Venn diagram of DEGs between scRNAseq and reference RNAseq for the different timepoints and tissues. D, Venn diagram of DEGs between ED and EN for scRNAseq and reference RNAseq. DEGs are defined as |log2FC| ≥ 1 and FDR of 0.05.