Extended Data Fig. 1: Development of CellTag-multi for parallel capture of lineage with scRNA-seq and scATAC-seq.
(a) Schematic comparing the original7,16 CellTag lineage tracing construct to the CellTag-multi construct. (b) Left Panel: Detailed flow chart and schematic of the modified scATAC-seq library preparation protocol. Right Panel: Major molecular steps of the protocol and the final library containing both CellTag and chromatin accessibility fragments. (c) Bar plot comparing total number of CellTag reads per library obtained across different scATAC-seq library preparation methods. Each library was sequenced to a similar sequencing depth. (d) Mean percent cells with at least one CellTag detected in scATAC-seq, relative to scRNA-seq (n=2 samples/assay). Plots for (e) fragment size distribution and (f) various scATAC-seq quality metrics across two datasets generated using the ‘original’ and ‘modified’ scATAC-seq library preparation method (nFrags/cell: number of unique fragments per cell; FRiP: Fraction of reads in Peaks; Cell numbers – Original: 1000; Modified: 977). Boxplots: center line, median; box limits, first and third quartiles; whiskers, 1.5x interquartile range. (g) Schematic of the species mixing experiment to assess purity of CellTag signatures in scATAC-seq. (h) Bar plot depicting distribution of CellTag reads across, human, mouse, doublet and non-cell droplets for the two CellTag libraries. We observed that the majority of CellTag reads mapped to the expected species of origin, 87.2% for the mouse library and 91.4% for the human library. (i) Bar plot showing cross-talk levels (Methods) across the human and mouse cells profiled. (j) Line plots showing relative abundance of individual CellTag barcode across the four plasmid library preparations. The four individual libraries were pooled to obtain the final high complexity CellTag-multi library.
