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A Targeted Multi-Omic Analysis Approach Measures Protein Expression and Low Abundance Transcripts on the Single Cell Level

45 Pages Posted: 29 Jul 2019 Publication Status: Published

See all articles by Florian Mair

Florian Mair

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Jami R. Erickson

Fred Hutchinson Cancer Research Center

Valentin Voillet

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Yannick Simoni

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Timothy Bi

Fred Hutchinson Cancer Research Center

Aaron J. Tyznik

BD Biosciences

Jody Martin

BD Biosciences

Raphael Gottardo

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Evan W. Newell

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division; Agency for Science, Technology and Research (A*STAR) - Singapore Immunology Network (SIgN)

Martin Prlic

Fred Hutchinson Cancer Research Center

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Abstract

High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcript, but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets. Here, we describe a novel targeted transcriptomics approach that combines analysis of over 400 genes with simultaneous measurement of over 40 proteins on more than 25,000 cells. This targeted approach requires only about 1/10 of the read depth compared to a whole transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic transcript-protein datasets, we adapted One-SENSE for intuitive visualization of the relationship of proteins and transcripts on a single-cell level.

Keywords: sc-RNA sequencing, multi-omic, AbSeq, high-dimensional cytometry, human immunology

Suggested Citation

Mair, Florian and Erickson, Jami R. and Voillet, Valentin and Simoni, Yannick and Bi, Timothy and Tyznik, Aaron J. and Martin, Jody and Gottardo, Raphael and Newell, Evan W. and Prlic, Martin, A Targeted Multi-Omic Analysis Approach Measures Protein Expression and Low Abundance Transcripts on the Single Cell Level (July 25, 2019). Available at SSRN: https://ssrn.com/abstract=3426658 or http://dx.doi.org/10.2139/ssrn.3426658
This version of the paper has not been formally peer reviewed.

Florian Mair

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Seattle, WA 98109-1024
United States

Jami R. Erickson

Fred Hutchinson Cancer Research Center

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Valentin Voillet

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Yannick Simoni

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Seattle, WA 98109-1024
United States

Timothy Bi

Fred Hutchinson Cancer Research Center

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Aaron J. Tyznik

BD Biosciences

La Jolla, CA 92037
United States

Jody Martin

BD Biosciences

La Jolla, CA 92037
United States

Raphael Gottardo

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division ( email )

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Evan W. Newell

Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division

Seattle, WA 98109-1024
United States

Agency for Science, Technology and Research (A*STAR) - Singapore Immunology Network (SIgN)

1 Fusionopolis Way
#16-16 Connexis
Singapore, 138632
Singapore

Martin Prlic (Contact Author)

Fred Hutchinson Cancer Research Center ( email )

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

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