Recording temporal data onto DNA with temporal resolution

We use a template-independent DNA polymerase, terminal deoxynucleotidyl transferase (TdT) that adds dNTPs to single-stranded DNA (ssDNA) substrates to build a biorecording system called TURTLES, TdT-mediated Untemplated Recording of Temporal Local Environmental Signals. We show that in vitro, the base-incorporation preference of TdT is sensitive to signals such as temperature as well as the presence of Ca2+, Co2+, and Zn2+. We use this difference in base preference to record a given signal. The structure of each sequence is 5' PE1 - CS1 - Extension - CS2 - PE2 3'. Sequenced on an Illumina MiniSeq Mid Output flow cell. See GitHub repository for filtering and trimming code as well as analysis code.