Transposition Selection Guidelines

The GEM-X Epi Multiome assay accommodates a wide range of nuclei inputs, supporting both Individual Transposition (input ≤30,000 for 500-20,000 Targeted Nuclei Recovery from GEMs) & Scalable Transposition (input ≥30,000 for 20,000–75,000 Targeted Nuclei Recovery from Transposition). Both Individual and Scalable Transposition workflows are similar with few key differences summarized below along with an example. Choose one based on sample and experimental goals.

Parameters	Individual Transposition	Scalable Transposition
Starting nuclei input	Lower (≤30,000) Individual Transposition – Nuclei Input Calculator	Higher (≥30,000) Scalable Transposition – Nuclei Input Calculator
Targeted nuclei recovery	500-20,000 from Transposition + GEM Generation	20,000-75,000 from Transposition
Transposed nuclei resuspension volume	25 μl	35 μl
Transposed nuclei concentration	Not determined	Determined (using 5 μl nuclei suspension)
Execution	Individual Transposition	Scalable Transposition
GEM-X Chip loading	25 μl Transposed nuclei	Volume based on adjusting nuclei concentration
Replicates during GEM Generation	Not feasible	Feasible

The workflow example illustrates two different nuclei input amounts. Some nuclei loss is expected during the post transposition wash step. This example assumes ~10% nuclei loss but this will vary between users and starting sample.