Aim for E. coli Spike-in DNA to comprise ~1% (0.5-5%) of total sequencing reads. In the protocol, 0.5 ng is recommended for 500,000 cells. Generally, this can be decreased linearly with decreasing cell number (e.g. 0.1 ng per 100,000 cells). The amount may need to be adjusted to achieve read counts in the optimal range due to variables such as target abundance, antibody efficiency, etc.
How many reads do I need for E. coli Spike-in DNA?
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