She received a B.A. in Biological Sciences at Smith College in 2001, and then conducted her graduate studies at the University of California, San Diego where she studied DNA mismatch repair under the supervision of Richard Kolodner and received a Ph.D. in Biomedical Sciences in 2008. Scarlet then received postdoctoral training in the lab of Sarah Fortune at the Harvard T. H. Chan School of Public Health, where she investigated the role of DNA methylation in Mycobacterium tuberculosis and developed methodology to map mycobacterial transcription start sites and RNA cleavage sites transcriptome-wide.