Table 1.

Overview of Affymetrix studies used for final transcriptome analysis. Studies are presented in chronological order. Each row represents a separate model

GSEid	Reference	Platform	No. of samples	Device	Cell system	Flow	Oxygen	Culture time	Microbiome? If yes, species and number
GSE7259	(Dihal et al. 2007)	Human Genome U133A 2.0 Array	4	Insert	Caco-2	Static	Oxic	Short; Medium	No
GSE15636	(Putaala et al. 2010)	Human GENOME U133 PLUS 2.0 ARRAY	17	Insert	Caco-2	Static	Oxic	Short	L. acidophilus NCFM (Bacterium 1, strain B and SN), B. lactis (Bacterium 4 and SN), L. salivarius (Bacterium 5 and SN)
GSE17625	(Ishimoto et al. 2010)	Human Genome U133 Plus 2.0 Array	6	Insert	Co-culture	Static	Oxic	Medium	No
GSE21976	(Turroni et al. 2010)	NuGO array (human) NuGO_Hs1a520180	8	Insert	Caco-2	Static	Anoxic apical compartment	Short	B. bifidum PRL2010 (Bacterium 7)
GSE30292	(Christensen et al. 2012)	Human Genome U133 Plus 2.0 Array	3	Insert	Caco-2	Static	Oxic	Long	No
GSE30364	(Rossi et al. 2013)	Human Genome U133 Plus 2.0 Array	3	Insert	Caco-2	Static	Oxic	Medium	No
GSE65790	(Kim et al. 2016)	Human Gene 1.0 ST Array	2	Insert	Caco-2	Static	Oxic	NR	No
		Human Gene 1.0 ST Array	4	Chip	Co-culture	Dynamic	Oxic	Short	VSL#3 (Bacterial community 1)
GSE79383	(Shah et al. 2016)	Human Transcriptome Array 2.0	9	Chip	Caco-2	Dynamic	Anoxic apical compartment	Short	L. rhamnosus GG (Bacterium 7), LGG + B. caccae (Bacterium 7 and 8), separated by PC membrane
GSE81867	(Sakharov et al. 2019)	Human Gene 1.0 ST Array	3	Insert	Caco-2	Static	Oxic	Short	No
		Human Gene 1.0 ST Array	3	Insert	Caco-2	Part. Dynamic	Oxic	Short	No
GSE115022	(Lépine et al. 2018)	Human Gene 1.1 ST Array	8	Insert	Caco-2	Static	Oxic	Long	L. acidophilus W37 (Bacterium 1, strain A), L. brevis W63 (2), L. casei W56 (3)
GSE156269	(Kulthong et al. 2021a)	Human Gene 2.1 ST array	4	Insert	Caco-2	Static	Oxic	Long	No
		Human Gene 2.1 ST array	4	Chip	Caco-2	Dynamic	Oxic	Long	No
GSE158620	(Kulthong et al. 2021b)	Human Gene 2.1 ST Array	8	Chip	Caco-2	Dynamic	Oxic	Long	No
		Human Gene 2.1 ST Array	8	Insert	Caco-2	Static	Oxic	Long	No
GSE173729	(Elzinga et al. 2021)	Human Gene 1.1 ST Array	3	Insert	Caco-2	Static	Oxic	Medium	No
		Human Gene 1.1 ST Array	3	Insert	Caco-2	Dynamic	Oxic	Medium	No