Question: I have a low starting number of cells. Should I process my sample using the LT or the standard Single Cell Gene Expression kit?
Answer: If starting with a very low number of cells going into GEM generation, fewer cells will be recovered with the LT kit compared to the standard kit, due to the lower capture rate. The capture rate for the LT kit is 35%, compared to 65% for the standard kit. Therefore, kit selection should be based on the goal of the experiment, and not on the starting number of cells.
If the goal of the experiment is to perform a pilot study, optimize sample prep, or perform a trial run of the workflow, the LT kit presents a cost-effective method of performing these experiments. If the goal of the experiment is to get the most cells out of an important sample, then the standard kit, with a higher recovery rate, may be the better option.
Whichever kit is selected, achieving the targeted cell number depends on many factors, including accurate cell counting, ensuring samples have high viability, and minimizing stress during sample preparation.
In rare cases, low RNA containing cells may not be called by our normal cell-calling algorithm. In these cases, it is possible to analyze the data using --force-cells; however, we recommend careful analysis of the data generated via this method to ensure that it is biologically meaningful.
Products: Single Cell Gene Expression