GEM-X Flex v2 offers comprehensive scalable solutions to measure gene and protein expression in samples that are fixed with formaldehyde. This document provides workflow overviews, document resources, reagents, and consumables for the GEM-X Flex v2 protocols. This document also provides guidance on selecting the appropriate sample preparation and library construction protocols for different workflows. An overview of the GEM-X Flex v2 data analysis is also included in this document. The 10x Genomics GEM-X Flex v2 Reagent Kits are not listed in this document.