Question: How can I test whether my cells can be partitioned into GEMs?
Answer: If your cells are large and you are concerned they may not be partitioned into GEMs, it is possible to use the Chromium Controller Training Kit to determine if your cells can be partitioned. (The reason this will not work with actual reagent kits is because the cells will be lysed as soon as they partition into GEMs).
If you decide to try this, we would suggest using a cell stain or fluorescent dye to make visualizing the cells in GEMs easier. After running the Training Chip with your sample, the GEMs can be visualized with a microscope to inspect the GEMs for cells.
An important point to remember is that depending on cell loading, only 1-10% of GEMs will contain a cell.
Products: Single Cell 3', VDJ