Fig. 2: Specific expression of marker genes for hypocotyl cell types and lateral root caps.

a, Expression of AT4G18970 in hypocotyl epidermal cells under dark and light conditions. The gene expression pattern was determined by AT4G18970 promoter-driven Histone2B-GFP (H2B-GFP, green) reporter. The cell outline (red) was visualized by FM4-64 staining in addition to DsRed2 reporter driven by a seedling-specific promoter (pAT2S3). b, Expression of AT3G05150 in hypocotyl cortical cells specifically in darkness. The gene expression pattern was determined using Histone2B-GFP (H2B-GFP, green) reporter driven by AT3G05150 promoter. The cell outline (red) was visualized by FM4-64 staining in addition to DsRed2 reporter driven by a seedling-specific promoter (pAT2S3). c, Expression of AT1G78450 in hypocotyl cortical cells specifically in light conditions. The gene expression pattern was determined by AT1G78450 promoter-driven Histone2B-GFP (H2B-GFP, green) reporter. The cell outline (red) was visualized by FM4-64 staining in addition to DsRed2 reporter driven by a seedling-specific promoter (pAT2S3). d, Expression of AT1G53708 in subtype LRC1 and LRC2 in dark and light conditions, respectively. The seedling cells (red) were labelled with the seedling-specific promoter AT2S3::DsRed2. e, Expression of AT4G13890 in a stable subtype LRC3 in dark and light conditions. The seedling cells (red) were labelled with the seedling-specific promoter AT2S3::DsRed2. The expression patterns of marker genes in cell atlases for Dark and Light samples are correspondingly illustrated on the right. Colour bar, normalized UMI counts; darker colours indicated higher expression. Scale bar, 100 μm. Each experiment was independently repeated three times.