Fig. 1

Graphical overview of the presented workflows. A. Accessible chromatin feature definition. The analysed brain regions are listed and shown in colour on the schematic of mouse embryo. Samples were collected from the telencephalon (Tel) and diencephalon (Di), midbrain (MB) and rhombomere 1 (R1) regions of E14.5 mouse embryos and used as indicated in each workflow. The process for defining the ATAC feature space across studied brain regions is described, showing the methods and steps of the workflow. See Methods for details. The circosplot shows the density of features (yellow) across the mouse karyotype. Boxplot shows the distribution of features by feature length in base pairs (bp). Outliers (> Q3 + 1.5*IQR) were excluded from the boxplot. B. Schematic of the scRNA-seq and scATAC-seq data processing and integration workflow. Samples (number of replicates indicated) were subjected to single-cell mRNA-seq (scRNA-seq) or single-cell ATAC-seq (scATAC-seq). Each replicate consists of ca 5000 cells (scRNA-seq) or nuclei (scATAC-seq) from a single embryo. The sequencing reads from scRNA-seq (red outlines) or scATAC-seq (black outlines) are first processed in parallel, then combined into an integrated object. The scATAC-seq data is scored along the previously defined E14.5 ATAC features. scRNA-seq data is scored along the mouse genes. After clustering resolution optimisation using ChooseR, the scRNA-seq data is integrated with scATAC-seq using Seurat/Signac so that scATAC cells are linked to expression values interpolated from scRNA and scRNA cluster labels are label transferred as additional metadata to scATAC-object. Integration is followed by the optimisation of the clustering based on ATAC features (ChooseR). Cell type classification (scType) and marker definition (CombiROC) is done after the integration of scATAC-seq and scRNA-seq data. Tel, telencephalon (yellow); Di, DI, diencephalon (yellow); MB, midbrain (green); R1, rhombomere 1 (blue). LSA, Latent Semantic Analysis; QC, Quality Control; PCA, Principal Component Analysis; scATAC, scATAC-seq, single-cell ATAC-sequencing; scRNA, scRNA-seq, single-cell mRNA-sequencing