We found that nine lncRNA–mRNA pairs were differentially expressed upon E. coli infection, and all of them showed concordant patterns of expression, including seven upregulated pairs (RP11-442H21.2/DDIT4, RP11-624G17.3/RTN4RL2, RP11-796E2.4/BTG1, RP11-809N8.2/RELT, RP4-781K5.2/IRF2BP2, AC093673.5/ZYX, and RP11-445F12.1/LHX1) and 2 downregulated pairs (CTD-2540B15.11/CEBPA and RP11-1143G9.4/LYZ) (Fig. 1b and c) (Table S5). Here, RTN4RL2 is linked to escherichia coli infection.