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

Xu, Z.; Heidrich-OHare, E.; Chen, W.; Duerr, R. H.

doi:10.1101/2021.12.15.472792

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bioRxiv · 10.1101/2021.12.15.472792

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

Xu, Z.·Heidrich-OHare, E.·Chen, W.·Duerr, R. H.

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Abstract

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.

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Xu, Z., Heidrich-OHare, E., Chen, W., Duerr, R. H.. 2021-12-16. Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics. https://doi.org/10.1101/2021.12.15.472792

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