Journal: bioRxiv
Article Title: The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
doi: 10.1101/2020.07.17.204792
Figure Lengend Snippet: (A) UMAP dimensionality reduction plot of root cells using peak-level scATAC data. Cells are colored according to Louvain clusters, and broad tissue types are indicated with transparent shading. (B) Pseudo-bulked peak tracks generated by combining ATAC data from all cells within a cluster. Each column represents a single locus in the genome that shows cell type-specific accessibility; each row represents a cell type, and each column shows an example marker peak for each type. Colors match those in previous panel. A cluster residing between the epidermis and endodermis clusters, with expression of markers from both cell types ( Figure S2B, S2C ) was given the label ‘c/e pre’ (precursor of cortex/endodermis, second row), and epidermis was shortened to ‘epi’. (C) Dotplot showing marker genes for each cell type cluster. Each column represents a single gene’s activity score, the summed accessibility of its gene body and promoter sequence (−400bp from transcription start site). The color of each dot indicates the magnitude of accessibility and the size of each dot represents the fraction of cells in each cell type showing accessibility at that gene. (D) Heatmap showing the predicted effect, across all peaks, of motifs from each Arabidopsis transcription factor family on cell type-specific accessibility. Darker shades of red indicate that presence of the motif is correlated with increased accessibility in that cell type, whereas shades of blue indicate that the motif is anti-correlated with accessibility. The mean effect all transcription factors within a given family are shown as rows, and each column represents a cell type.
Article Snippet: Nuclei yield with this protocol was ∼ 94,000 nuclei per gram of roots (fresh weight). scATAC-seq libraries were built using the 10x Genomics Chromium Single Cell ATAC Solution platform, following manufacturer’s recommendations.
Techniques: Generated, Marker, Expressing, Activity Assay, Sequencing
