High background in sequencing data could indicate poor sample or library prep, over-digestion by MNase, DNA damage, or antibody failure.
To troubleshoot this, use 500,000 cells per reaction, including reactions with control antibodies and the K-MetStat Panel. Read the tips below:
Confirm sample prep and include all recommended controls and success metrics.
Process cells quickly and resuspend in cold Antibody Buffer.
Test multiple antibodies to experimental target.
Ensure MNase digestion is incubated at 4˚C for 2 hours.
Keep adapter ligation reagents on ice during ligation setup.
Double check that library prep PCR parameters are accurate.