Table 1 Expression (TPM) in colon organoids of a subset of genes that are expected to be expressed in the porcine colon and/or that had been studied in a study on ex vivo LPS challenge of porcine colon tissue [20, 22]. A number of these genes were not (or hardly) expressed in the colon organoids are in bold (TPM values < 1). Genes that showed a significant response to E coli challenge are shown underlined and bold. Full list of expression of colon specific genes retrieved from TiGER database can be found in Additional file 2

Expected colon genes

ACTA2

0.08 ± 0.08

0.11 ± 0.12

0.08 ± 0.12

0.07 ± 0.10

ANTXR1

1.62 ± 1.12

2.49 ± 1.93

2.11 ± 1.28

3.34 ± 2.66

CALD1

54.72 ± 36.22

59.76 ± 29.02

67.33 ± 38.99

66.70 ± 33.09

CDX2

17.33 ± 11.11

14.66 ± 10.12

11.68 ± 10.28

9.14 ± 7.05

CFTR

7.10 ± 4.71

6.92 ± 4.52

10.96 ± 5.95

9.58 ± 6.07

CHGA

2.67 ± 3.79

2.79 ± 3.26

2.26 ± 3.79

2.93 ± 4.35

GLP2R

0.70 ± 0.35

0.82 ± 0.30

0.51 ± 0.25

0.52 ± 0.20

HOXA3

0.54 ± 0.38

0.69 ± 0.30

0.65 ± 0.46

0.64 ± 0.26

HOXD9

1.09 ± 0.59

1.06 ± 0.73

0.97 ± 0.47

0.62 ± 0.25

KRT20

34.19 ± 30.78

35.89 ± 28.65

22.61 ± 23.80

27.23 ± 19.80

MTOR

13.14 ± 2.18

14.02 ± 2.66

16.99 ± 3.50

16.97 ± 2.33

NIFK

104.67 ± 12.52

106.96 ± 10.46

96.14 ± 13.19

96.23 ± 10.89

PECAM1

1.33 ± 0.81

1.18 ± 0.20

1.17 ± 0.68

0.97 ± 0.18

SDC1

232.00 ± 44.53

240.94 ± 41.92

263.98 ± 54.44

240.54 ± 56.73

SLC16A1

115.71 ± 24.37

118.54 ± 18.55

131.42 ± 35.62

129.58 ± 18.90

SLC44A4

152.29 ± 73.96

124.00 ± 53.94

153.80 ± 88.09

124.18 ± 55.10

SLC5A1

9.24 ± 2.91

6.61 ± 1.85

8.96 ± 2.74

7.36 ± 2.43

SLC9A3

1.11 ± 1.20

0.41 ± 0.34

0.91 ± 1.61

0.25 ± 0.15

WNT5B

3.89 ± 2.53

4.81 ± 3.25

4.62 ± 2.47

4.94 ± 3.67

Immunity related genes

FOS (AP1)^a

32.09 ± 5,86

39.63 ± 9,08

92,81 ± 28,12

97,19 ± 34,11

FOSB (AP1)^a

0,14 ± 0,19

0,13 ± 0,11

0,6 ± 0,56

0,59 ± 0,25

FOSL1 (AP1)^a

42,19 ± 22,80

48,76 ± 20,08

78,84 ± 38,01

88,87 ± 20,62

FOSL2 (AP1)^a

57,93 ± 10,55

57,41 ± 7,73

74,53 ± 8,87

73,94 ± 5,42

JUNB (AP1)^a

176,52 ± 25,24

193,03 ± 43,28

315,41 ± 156,88

306,77 ± 91,08

CLDN2

0.94 ± 0.51

1.02 ± 0.73

0.55 ± 0.36

0.72 ± 0.44

CXCL8

183.83 ± 123.61

221.65 ± 198.37

1968.36 ± 599.07

2549.55 ± 724.44

FFAR2

0

0

0

0

IFNG

0

0

0

0

IL1A

16.97 ± 8.84

15.44 ± 2.61

110.22 ± 49.75

112.59 ± 46.72

IL6

0.34 ± 0.28

0.72 ± 0.50

0.63 ± 0.69

1.05 ± 0.96

IL10

0

0

0

0

JAK2

23.10 ± 6.71

20.83 ± 1.89

21.23 ± 3.86

19.02 ± 1.70

NFAM1

0

0

0.01 ± 0.03

0

SOCS1

2.31 ± 0.99

1.48 ± 0.51

2.25 ± 1.10

2.14 ± 1.33

SOCS3

3.77 ± 1.34

3.78 ± 0.56

3.39 ± 1.95

2.83 ± 0.84

SOCS4

13.79 ± 1.94

13.92 ± 1.16

12.22 ± 1.59

11.76 ± 0.98

SOCS5

7.29 ± 0.64

7.29 ± 0.72

7.48 ± 1.12

6.81 ± 0.79

SOCS6

30.75 ± 6.90

31.16 ± 4.35

28.65 ± 4.65

28.33 ± 2.15

TLR1

2.10 ± 0.96

2.02 ± 0.82

1.73 ± 0.67

1.65 ± 0.71

TLR4

9.73 ± 1.95

9.92 ± 2.26

15.32 ± 4.78

15.04 ± 3.81

TLR6

1.28 ± 0.49

0.91 ± 0.46

0.95 ± 0.45

0.72 ± 0.24

TLR8

0.00 ± 0.01

0.00 ± 0.01

0.01 ± 0.01

0.01 ± 0.01

TNF

0.63 ± 0.52

0.57 ± 0.49

20.64 ± 6.99

24.89 ± 20.35

TRAM1

163.73 ± 24.60

165.57 ± 23.23

143.78 ± 15.86

151.46 ± 12.43