Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics

Area of Science:

• Single-cell multi-omics
• Immunology
• Molecular biology

Background:

• New multi-omics technologies like TEA-seq and DOGMA-seq offer insights into cell biology.
• Independent evaluation of these novel assays is crucial for their adoption.
• Understanding T cell activation requires detailed molecular profiling.

Purpose of the Study:

• To evaluate the utility of DOGMA-seq compared to CITE-seq in human peripheral blood T cells.
• To compare different permeabilization methods for single-cell multi-omics assays.

Main Methods:

• Single-cell trimodal omics (DOGMA-seq) and bimodal omics (CITE-seq) were performed on activated human T cells.
• Two permeabilization conditions, digitonin (DIG) and low-loss lysis (LLL), were tested for DOGMA-seq.
• ATAC-seq, mRNA, and cell surface protein libraries were generated and analyzed.

Main Results:

• Single-cell trimodal omics measurements using digitonin (DIG) permeabilization yielded better results than low-loss lysis (LLL).
• DOGMA-seq with optimized DIG permeabilization provided more ATAC-seq information compared to CITE-seq.
• CITE-seq demonstrated slightly superior quality for mRNA and cell surface protein libraries compared to DOGMA-seq.

Conclusions:

• DOGMA-seq is a valuable tool for single-cell multi-omics, particularly for ATAC-seq analysis in T cells.
• Permeabilization method choice significantly impacts data quality in single-cell omics assays.
• DOGMA-seq and CITE-seq offer complementary strengths for comprehensive T cell profiling.