Problem	Possible Cause	Solution
Step 3.3) Cannot form GΩ seal	Surface of cell is not clean enough	Clean further using positive pressure
Step 3.3) Cell appears to deflate/die		Prepare new pipette and target a new cell
Step 3.4) Cannot determine terminal location of dendrites	Alexafluor has not had enough time to diffuse throughout cell or concentration of Alexafluor is not high enough	Check to make sure gain and exposure time on camera are high enough. Wait an additional 5 min before visualizing dendrites. If dendrites still are not visible, prepare solution with higher Alexafluor concentration.
Step 4.1) Unable to aspirate all of cytoplasm
Step 5.5) Supernatant is not clear after 8 minutes		Gently pipette entire solution twice, while still on magnetic separator, and let sit for another 5 min
Step 5.5) Pellet disperses during pipetting	Sample is too far from magnet	Keep tubes on magnetic separating device during all pipetting. Expel solution and allow beads to re-pellet for 5 min
Step 5.7) After 5 min, samples still appear glossy	Maximum amount of EtOH has not been removed	Continue to monitor samples during drying. Every 2 min, use a P10 pipette and remove all EtOH at bottom of tube
Step 8.9) Pellet had cracks before rehydration		Allow sample to rehydrate for a total of 4 min, rather than 2 (Step 8.10)
Step 8.11) Small amount of bead was brought up with supernatant		Eject entire sample back into tube and place on magnetic separator for 1 min; Pipet up gently and make sure to avoid pellet
Step 8.12) DNA smears are inconsistent and fluorescence scale continuously changes	Too high DNA concentration for a HS chip	Check concentration of sample and dilute between 1 - 10 ng/µL. Rerun bioanalyzer
Step 8.12) Low molecular weight smear	RNA Degradation	Make sure to flash freeze cell immediately after collection. Discard this cDNA library
Step 8.12) Fluctuating marker baseline in control lane	Contamination or old reagent	Discard DNA marker and employ new tube for Bioanalyzer run
Step 8.12) No DNA smear	Failure to expel cell	Pull new needles with a slightly larger tip
	RNA Bead Failure	Make sure beads have been fully resuspended before use and allow samples to incubate before placing on magnetic separator
Step 8.12) Weak DNA smear	Not enough amplification	Employ more PCR cycles
Step 8.12) DNA smear outside of 500bp-2Kb range		DNA smears below 0.5 and above 2 Kb are likely contamination. Discard sample
Step 8.12) Regularly spaced spikes on DNA trace	Contamination of sample	Always wear fresh gloves and make new ethanol for rinses; filter tips should be used at all times
Step 9.3) Unable to detect concentration of sample on fluorometer		Samples below detection level have too little DNA for tagmentation and cannot be used
Step 10.10) Samples are not dry after 10 min	Continue to remove excess EtOH	Allow samples to airdry longer, check on them every minutes
Step 10.13) Smear skewed toward 2Kb	Incomplete fragmentation	Re-dilute sample to a concentration of 0.15 ng/µL, rather than 0.2 ng/µL; rerun tagmentation
Step 10.13) Smear skewed toward 200bp	Too little DNA input	Dilute sample less, try a concentration of 0.4 ng/µL; rerun tagmentation
	Tagmentation reaction too long	Reduce reaction time of tagmentation to 8 min
Step 10.13) Weak smears	Improper Amplification of DNA	Dilute sample to concentration of 0.4 ng/µL and rerun tagmentation
Step 11.2) Maximum obtainable pool concentration is below 5 nM		Identify which sample(s) have significantly low concentrations and rerun tagmentation with new dilution