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Fig. 1 | Genome Biology

Fig. 1

From: Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

Fig. 1

Construction of single-cell transcriptional profile for the outer integument cells of the cotton ovule. a Schematic of the experimental design. A development period mixed sample (− 2DPA to 2DPA) of ovule outer integument cells from WT and fl were separately enzymatically digested for scRNA-seq and scATAC-seq sequencing. The OI, II, and ES denote the out integument, inner integument, and embryo sac of ovules, respectively. b UMAP projection of WT (left) and fl (right) scRNA-seq data. Clusters are labeled by color. The lost cell cluster in fl is marked with a dotted line circle. c Distribution of cell numbers for WT and fl scRNA-seq data in each cell cluster. d UMAP projection showing that the batch effect difference between data of different platforms is well eliminated. See also Additional files 2 and 3: Table S1-2. e The number of marker genes identified by scRNA-seq for transcriptional factors and non-transcriptional factors in each cell cluster. f The distribution of Moran’s I score for marker genes and other genes. The number of marker genes in each group and the p values from two-sided Wilcoxon tests between marker genes and other genes are shown at the top (* represent p < 1E − 3, ** represent p < 1E − 6, *** represent p < 1E − 9). g Heatmap showing normalized gene expression values for top 10 marker genes in each cell cluster. h In situ hybridization of XTH gene with RNA probes of antisense (left) and sense (right). The black triangles show the signals from fiber cells, scale bar = 300 μm. i A representative example illustrating the capture of fiber cells by laser-capture microdissection (LCM). The fiber cells indicated by star symbols were cut from the epidermis of an ovule at 1 DPA. Scale bar, 50 μm. j,k The gene expression correlation analysis between the cells in the UMAP and 1 DPA fiber cells of LCM-seq (j), and 5 DPA fiber cells of bulk RNA-seq (k) in three replicates. The Spearman correlation coefficients are shown for the cells in the UMAP of scRNA-seq from WT (top) and fl (bottom). The dotted line circle marks the C3 cell cluster from scRNA-seq

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