Simultaneous Quantification of Single-Cell Proteomes and Transcriptomes in Integrated Fluidic Circuits

Mandi Wong; Carol Kosman; Liane Takahashi; Naveen Ramalingam

doi:10.1007/978-1-0716-1771-7_15

Simultaneous Quantification of Single-Cell Proteomes and Transcriptomes in Integrated Fluidic Circuits

Methods Mol Biol. 2022:2386:219-261. doi: 10.1007/978-1-0716-1771-7_15.

Authors

Mandi Wong¹, Carol Kosman², Liane Takahashi², Naveen Ramalingam²

Affiliations

¹ Fluidigm Corporation, South San Francisco, CA, USA. mandi.wong@fluidigm.com.
² Fluidigm Corporation, South San Francisco, CA, USA.

PMID: 34766275
DOI: 10.1007/978-1-0716-1771-7_15

Abstract

Understanding the principles of gene regulation at single-cell resolution would require measurement and integration of multiple methods such as DNA mutation profiling, open chromatin profiling, RNA expression, protein quantification, and DNA methylation. Recent developments in single-cell multi-omic technologies have enabled integration of these modes in various combinations.With the advent of RNA expression and protein sequencing assay (REAP-seq), researchers can simultaneously analyze protein and gene expression within the same cell. In REAP-seq , cells are labeled with antibodies conjugated to unique DNA sequences. A barcode of 8 nucleotides can allow up to 65,536 unique barcodes for multiplex analysis of proteins, circumventing the limitations of fluorescence (~17 targets). Here, we describe the implementation of REAP-seq assay in the Fluidigm^® C1™ mRNA Seq HT (high-throughput) v2 system.

Keywords: Gene expression; Genomics; Immunology; Lymphocytes; Methods; Multi-omics; Protein expression; REAP-seq; RNA; Sequencing; Single cell analysis.

MeSH terms

Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Proteome* / genetics
RNA
Sequence Analysis, RNA
Single-Cell Analysis
Transcriptome*

Substances

Proteome
RNA