Supplementary figures and tables E g r 1 F g f2 F g f7 1 0 * 5 1 0 * * e e e * g g g * n n n * a a a 8 4 * 8 h h h * c c c d d d * l l l o o o * f f f * n n n o o o 6 3 6 i i i s s s s s s e e e r r r p p p x x x e e e 4 2 4 e e e n n n e e e g g g e e e v v v i i i t t t 2 1 2 a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d J a k 2 N o tc h 2 H if1 * 3 4 6 * * * e e e g g g n n n a a * * a * h h * h c c c 3 * d d * d l l l * o o o f f 2 f 4 n n n o o o i i i s s s s s s e e e r r 2 r p p p x x x e e e e e e n n n e e 1 e 2 g g g e e 1 e v v v i i i t t t a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Z e b 2 C d h 1 S n a i1 * * 7 1 .5 4 * * e e e g g g 6 n n n * a a a * h h h c c c 3 * d d d l l l 5 o o o f f f 1 .0 * n n n * o o o i i i 4 * s s s s s s e e e r r r 2 p p p x x x 3 e e e e e e n n n e e e 0 .5 g g g 2 e e e 1 v v v i i i t t t a a a * l l l e e e 1 * R R R 0 0 .0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d M m p 9 L o x V im 2 0 0 2 0 8 * * * e e e * g g g 1 5 0 * n n n * a a a * h h h * c c c 1 5 * 6 d d d l l l 1 0 0 o o o f f f n n n o o o i i i 5 0 s s s s s s * e e e r r r 1 0 4 3 0 p p p * x x x e e e * e e e n n n e e e 2 0 g g g e e e 5 2 v v v i i i t t t a a a l l l 1 0 e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Supplementary Figure 1. Validation of RNA-Seq results by the comparison to our previous QPCR results related to epithelial-to-mesenchymal transition [13, 15]. The relative gene expression of Egr1, Fgf2, Fgf7, Jak2, Notch2, Hif1α, Zeb2, Cdh1, Snai1, Mmp9, Lox and Vim is shown from control (left columns), uninflamed (middle columns) and inflamed (right columns) rat colon sections. White and black columns represent RNA-Seq and previously published QPCR data, respectively. Data are presented as the mean ± SEM; *p < 0.05. 1 Supplementary table 1 List of significantly activated canonical pathways in the in vivo rat model of IBD based on p-value, calculated by Ingenuity Pathway Analysis (IPA) application. The abbreviations “UI—C,” “I—C” and “I—UI” represent the TNBS treated—uninflamed vs. control, TNBS-treated—inflamed vs. control and TNBS treated—inflamed vs. TNBS treated—uninflamed comparisons. 2 Supplementary Table 2. List of significantly activated canonical pathways in the in vivo rat model of IBD based on z-score, calculated by IPA application. Abbreviations as “UI—C,” “I—C” and “I—UI” represent the TNBS treated—uninflamed vs. control, TNBS-treated—inflamed vs. control and TNBS treated—inflamed vs. TNBS treated—uninflamed comparisons. 3 Supplementary Figure 2. Expression pattern of NOD-like receptors in experimentally induced colitis. Heat map shows gene expression alteration of NLR receptors between control, TNBS- treated uninflamed and TNBS-treated inflamed rat colon samples, where red marks elevation, while blue marks decrease by at least two-fold in expression level; false discovery rate (FDR) < 0.05. Bar plots show the expression alteration of Nod2, Nlrp3, Nlrp6 and Nlrc4 between rat sample groups; white and black columns represent RNA-Seq and QPCR data, respectively, *p < 0.05. Abbreviations as “UI—C,” “I—C” and “I—UI” represent the TNBS treated—uninflamed vs. control, TNBS-treated—inflamed vs. control and TNBS treated—inflamed vs. TNBS treated—uninflamed comparisons. 4 F u t1 F u t2 * 1 .5 4 * * e e * g g n n a a * h h c c 3 d d l l o o f 1 .0 f n n o o i i s s s s e e r r 2 p p x x e e e e n n e 0 .5 e g g e e 1 v v i i t t a a l * l e e * R * R 0 .0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d F u t4 F u t9 * * 3 * 2 5 * e * e * g g n n a a 2 0 h h c c d d l l * o o f f 2 n n 1 5 o o i i s s s s e e r r 3 p p x x e e e e * n n e e 1 2 g g e e v v i i t t a a l l 1 e e R R 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Supplementary Figure 3. Diverse expression pattern of FUTs at the site of colon inflammation in rat experimental colitis. The relative gene expression of Fut1, Fut2, Fut4 and Fut9 is shown from control (left columns), uninflamed (middle columns) and inflamed (right columns) rat colon sections. White and black columns represent RNA-Seq and QPCR data, respectively. Data are presented as the mean ± SEM; *p < 0.05. 5 Il1 Il6 Il1 0 4 0 0 2 0 1 2 0 * e e 3 5 0 e g g * g * n n n 1 0 0 a a a 3 0 0 h h * h * c c c 1 5 d d d l l l 2 5 0 o o o f f f 8 0 n n n 2 0 0 o o o i i i s s s s s s e e 1 5 0 e r r 1 0 r 6 0 3 0 * p p p * x x x e e e e e e * * n n n e e e 4 0 2 0 g g g * e e e 5 v v v i i i t t t a a a l l l 2 0 1 0 e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d C x c l1 T n f T n fa ip 6 5 0 8 * 1 0 * * * e e e * g g g * n n n * a a a 4 0 8 h h h * c c c * 6 d d d l l l * o o o f f f n n n o o o 3 0 6 * i i i s s s s s s e e e * r r r 4 p p p x x x e e e 2 0 4 e e e n n n e e e g g g e e e 2 v v v i i i t t t 1 0 2 a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Supplementary Figure 4.