Transcriptome of E. coli K12: 15 M Cu and 30 M Ni exposure, replicate 2
E. coli cultures grown until they reached an OD of 0.25-0.3 (mid-exponential phase). Cultures were then treated for 2 hours with one of the following conditions: (1) Control (no treatment), (2) 30 M Ni, (3) 15 M Cu, (4) 30 M Ni and 15 M Cu. After treatment, cultures were centrifuged at 10,000 rpm for 5 minutes, the supernatant was discarded, and the pellet was washed twice with phosphate-buffered saline (PBS). The washed pellet was resuspended in 1 mL of PBS, transferred to 2 mL sterile Eppendorf tubes, and centrifuged again. RNA was immediately extracted using the Zymo Quick-RNA Miniprep Kit, following the manufacturers protocols. RNA samples were immediately frozen at -80C prior to further analysis. . For library preparation, the Ribo-off rRNA Depletion Kit V2 (Bacteria) (N417, Vazyme, Nanjing, China) was used for rRNA depletion. Then, the ALFA-SEQ Directional RNALibPrepKit (RL1020, Magigene, Guangzhou, China) was used, following the manufacturers recommendations. Library quality control was performed using the QSep-400 (BiOptic, Taipei, China) and Qubit 3.0 (Thermo Fisher Scientific, Wilmington, USA). The library was sequenced on the Illumina Novaseq platform (Illumina, San Diego, USA)with paired-end 150 bp (PE150) mode.