This upload contain the code, .tsv fragment files, .rds files, and other interpreted files necessary to reproduce the single cell analysis presented the revised MulTI-Tag manuscript (https://doi.org/10.1101/2021.07.08.451691). Figure 2 includes datasets for K562, H1 hESC, and mixed K562-H1 co-profiled for H3K27me3 and H3K36me3; and K562, H1 hESC, and mixed K562-H1 co-profiled for multiple target combinations in the same experiment (H3K27me3-PolIIS5P, H3K27me3-H3K9me3, H3K27me3-H3K4me1, H3K27me3-H3K36me3). Figure 3 includes datasets for K562 and H1 co-profiled for H3K27me3, H3K4me2, and H3K36me3. Figure 4 includes datasets for H1 hESCs differentiated to three germ layers (Ectoderm, Endoderm, and Mesoderm), with timepoints collected every 24 hours, and co-profiled for H3K27me3, H3K4me1, and H3K36me3.