Fig. 1: Germinating embryo scRNA-seq experimental design and impact of protoplast isolation on the transcriptome.
From: Establishment of single-cell transcriptional states during seed germination
a, Arabidopsis seed germination analysis showing the percentage rupture of different stages during seed germination by measuring testa rupture (red line) and endosperm rupture (green line). Representative images for each time point are shown below. b, Germination procedure and sampling for transcriptomic analyses: (1) RNA-seq of whole isolated embryos without protoplast isolation; (2) RNA-seq of embryo protoplasts; and (3) scRNA-seq of individual embryo protoplasts. c,d, Expression changes of 1,202 genes in response to protoplast isolation (log2[fold change]). The transcriptional response to protoplast isolation was consistent across time points (heatmap (c)) and included large fold-changes for well expressed genes (MA-plot (d)). e, Venn diagram of the limited overlap in upregulated genes upon protoplast isolation between this study and a previous study by Birnbaum and colleagues28. CPM, counts per million; np, non-protoplast; p, protoplast.
