Supplementary Figure 1: Data overview.
From: Dissecting cellular crosstalk by sequencing physically interacting cells
a, Experimental design of the in vitro model. OT-II CD4+ T cells were co-cultured with ovalbumin (OVA)-loaded, lipopolysaccharides (LPS)-exposed DC for 3, 20 and 44 hours. Mono-cultures of both cell types were used as controls. b, Projection of genes on the Metacell-generated 2d graph (Fig. 1c) allows identification of cell types by expression quantiles of Trbc2 (T cells) and Fscn1 (DC). c, Metacells distribution across MARS-seq technical replicates (rows), grouped by experimental condition and sorting scheme. Color bar indicates assignment of meta-cells to 9 T and DC subsets. d-g, summary of all MARS-seq plates and cells (Supplementary Table 1). Shown are (e) total number of Illumina reads, (f) total number of Unique Molecular Identifiers (UMI) per cell, and (g) fraction of QC-positive cells retained for further analysis per technical replicate. In (d), ‘Replicates’ indicate number of biological replicates (co-cultures or mice), ‘Batches’ indicate number of technical replicates, ‘%analyzed’ indicates fraction of QC-positive cells retained for downstream analysis.
