Question: How can I test whether my cells can be partitioned into GEMs?
Answer: The maximum cell size we have tested in-house is 30 um. However, samples have run successfully with cells >30um. The theoretical limit is the width of the microfluidic channel, which is ~50-60 um.
One way to determine if a new or unusual cell type can be partitioned into the GEMs is to test the cells using the Training Kit. The Training Kit is the same as the Single Cell Reagent Kit except that the training Gel Beads do not include lysis buffer. The partitioned cells are therefore expected to remain intact during GEM generation. The GEMs can be examined by microscopy for intact cells.
When using this method, it is important to keep in mind that at proper loading concentrations, only 1-10% of GEMs are expected to contain a cell.
Note: Cells that adhere to culture plates (adherent cells) contract once they are in solution and thus may differ in size. For example, neuronal cells may span across ~100 um when cultured in plates but will contract once in solution to a size that is applicable with the Single Cell assay.
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