Machine-learning guided discovery of emergent antimicrobial activity from dynamic covalent assemblies (Streptococcus mutans, RNA seq)

Streptococcus mutans ATCC25175 cells were collected after treatment under the indicated experimental conditions (e.g., A5B5 treatment and corresponding control groups), followed by centrifugation and PBS washing. Total RNA was extracted using the RNAprep Pure Cell/Bacteria Kit (TIANGEN, Beijing, China; Cat. No. DP430) according to the manufacturer’s protocol. RNA purity and concentration were measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only RNA samples with qualified purity, quantity, and integrity were used for library preparation. Ribosomal RNA was removed using the TIANSeq rRNA Depletion Kit (TIANGEN, Beijing, China). Strand-compatible transcriptome libraries were then prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit following the manufacturer’s instructions. Library sequencing was performed by OE Biotech Co., Ltd. (Shanghai, China).