Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative “low-loss lysis” (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells. For comparison between DIG and LLL conditions, eight aliquots of T cells were activated and stimulated separately. After labeled by hashtags, two groups of four aliquots of T cells were pooled together, stained by antibody cocktail, and permeabilized with DIG or LLL. For comparison between CITE-seq and DOGMA-seq, sixteen aliquots of T cells were activated and stimulated separately. After labeled by hashtags, two groups of eight aliquots of T cells were pooled together, stained by antibody cocktail, and subjected to CITE-seq or DOGMA-seq.