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Table S1. Experimental design for fluorescent dye labeling.

Table S2. Summary of average ratio of differentially expressed proteins in IBV (ck/CH/LDL/97I, H120)-, NDV (La Sota)- and AIV (H9)-infected groups and between IBV ck/CH/LDL/97I- and H120-infected groups.

Table S3. The primers for Real-time RT-PCR.

Table S4. Serological results post-inoculation with IBV (ck/CH/LDL/97I, H120), NDV (La Sota), and AIV (H9).

Table S5. Identification information of differentially expressed proteins in tracheal tissues of chickens infected with IBV (ck/CH/LDL/97I, H120), NDV (La Sota), and AIV (H9) identified by MALDI-TOF/TOF MS.

Table S6. Biological function annotation of differentially expressed proteins.

Table S7. Summary of up and down-regulated proteins during IBV (ck/CH/LDL/97I, H120), NDV (La Sota) and AIV (H9) infection, and proteins differentially expressed between IBV ck/CH/LDL/97I- and H120-infected groups.

Figure S1. Representative 2D-DIGE images of IBV (ck/CH/LDL/97I, H120)-, NDV (La Sota)-, and AIV (H9)-infected groups with their respective sampling points.

Figure S2. This file includes the PMF spectrum and confirmed MALDI-TOF/TOF MS spectrum of differentially expressed proteins.

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