Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa

Table 1 Number of DEGs in all in vitro and in vivo datasets and number of overlapping genes and pathways between in vivo and in vitro datasets

Comparison of treatments^a	Species (age)^b	Vitro concentration or dilution-factor diet (Rye)	Vivo concentration or dilution-factor diet (Rye)	Vivo^d day	Vivo^e	Vitro^e 2h/6h	Genes overlap 2h/6h	Pathways overlap 2h/6h
ZnO vs.Control^a	pig (weaned)	0.03125% w/v	0.25% w/w	23	101_36^c	174/720	4_1^c/3_3^c	7_1^c/2_0c
				35	11_11^c		0_1^c/2_1^c	2_3^c/2_4^c
Amoxicillin vs.Control^a	Broiler (1d)	0.5% w/v	0.0067% w/v	5	51	87/705	0/2	1/1
				14	36		0/1	2/2
rye 10% vs. 0%^a	Broiler (1d)	3	1	21	238	568/21	9/1	1/1
				28	219		8/0	3/3
rye 5% vs. 0%^a	Broiler (1d)	3	1	21	318	204/26	9/1	4/2
				28	34		1/0	0/0
rye 10% vs.5%	Broiler (1d)	3	1	21	47	455/17	0/0	1/0
				28	192		6/0	4/0

^aFor comparisons with IPEC-J2 cells, the ‘control’ (ZnO and amoxicillin) or ‘0%’ (rye) is a culture medium without additive or rye diet (except for the 10% rye vs. 5% rye comparison). For the ZnO in vivo experiment, the ‘contol’ is a regular diet with a normal level of Zn (60–100 mg/kg)
^bAge of broilers at the start of the rye and amoxicillin interventions and age of piglets (weaned) at the start of the animal experiment. Piglets were fed with a diet with a higher dose of zinc oxide (2500 mg/kg) from days 14 to 23 post-weaning
^cNumber of genes in the jejunum and number of genes in the ileum
^dNumber of days of sampling of intestinal tissue
^eNumber of DEGs with a p value <0.05 and absolute fold change of >2.0 or <0.5 in vitro and in vivo