Table 5 |.

Troubleshooting table for experimental procedures

Step	Problem	Possible reason	Solution
1A(i)	Failed timed pregnancy	The female mouse is not in proestrus or estrus	Setting up timed pregnancy for mice at estrous state can increase the likelihood of pregnancy
5	Low barcode induction efficiency in adults	The editing efficiency in adults varies among individuals	Prepare more induced adults and choose the ones with highest editing for DARLIN array analysis
8	The A260/280 ratio is low in RNA extraction	The organic phase is not removed completely	Do not pipette up the entire aqueous layer after phase separation
23	High-cluster density in sequencing	The complexity of the DARLIN library is low	Reduce the library loading concentration and add more PhiX
37	Poor sequencing read quality (reads PF <80% or Q30 <60%)	Overloaded sequencing. Lower loading concentrations may be required for single-cell DARLIN sequencing due to the long cycle number on read 2	Reduce library loading concentration
23,37	DNA present in water-only control	Cross-contamination of samples or contamination of one or more reagents with DARLIN DNA	Clean bench and pipettes with 10% bleach and/or use designated ‘clean’ library-preparation workspace. Ensure extreme care is taken to avoid cross-contamination of samples and reagents