Targeted Multi-Omics analysis and high-dimensional flow cytometry to measure protein expression and low-abundance transcripts at the single-cell level.

In this article published in Cell Reports, Mair et. al report a study on the use of targeted Multi-Omics to study immune-cell heterogeneity at a low sequencing depth. Working with sorted pan CD45+ live cells derived from cryopreserved PBMCs, the authors used a high-throughput (>104 single cells) approach in which they captured the cells in nano wells in the BD Rhapsody™ system, in combination with oligonucleotide conjugated antibodies (BD™ AbSeq). They simultaneously interrogated 492 immune-related genes and 41 surface proteins commonly used for immunophenotyping. Also, they performed 30-parameter flow cytometry to measure the expression of the same targets.

The authors found that the targeted approach was more efficient than WTA in detecting some of the low-abundance transcripts, requiring only one-tenth of the reading depth. This approach also enabled them to separate memory T cell subsets, as well as regulatory T cells (Tregs), something that is normally difficult to do due to the low amounts of mRNA that is recovered from T lymphocytes. The protein and transcription data were visualised in a single plot by adapting the one-dimensional soli expression by nonlinear stochastic embedding (One-SENSE). This technique allows effective visualisation and identification of cellular phenotypes differing by transcripts and proteins. The authors propose that the approach of targeted multi-omics combined with high-dimensional flow cytometry and the combined visualisation can constitute a methodological toolset for generating high-throughput, multi-omic, single-cell data with a focus on selected targets at minimal read depth.

Read the article in Cell Reports here.

 

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