Chromium Fixed RNA Profiling (Gene Expression Flex) with Feature Barcode technology offers comprehensive, scalable solutions to measure gene and protein expression in formaldehyde fixed samples. To measure protein expression, cell surface and intracellular proteins are labeled using an antibody conjugated to a Feature Barcode oligonucleotide, followed by a fixation with formaldehyde to ensure 1) the cells are properly fixed and permeabilized for probe hybridization and 2) the antibodies firmly bind to the cells, preventing their loss during probe hybridization.

This document outlines cell surface and intracellular protein labeling protocols for use with Chromium Fixed RNA Profiling. General guidance on antibody-oligonucleotide conjugation, evaluating antibodies with flow cytometry, and best practices when staining cells is also provided here.