Systems Approaches to Modeling Chronic Mucosal Inflammation

Table 1

Primer sequences in Q-RT-PCR assay.

Pathway	Gene	Accession #	Amplicon (bp)	Forward (5′-3′)	Reverse (5′-3′)
Canonical	NFKB1A	NM_020529	116	CCGCAGGAGGTGCCG	ATCACTTCCATGGTCAGTGCC
	CXCL2/GroB	NM_002089	100	ATTCACCTCAAGAACATCCAAAGTG	GCCCATTCTTGAGTGTGGCTAT
	TNFA1P3/A20	NM_001270508	111	GAAGCACCATGTTTGAAGGATACTG	CTCTGCGCTGGCTCGATC
	IL-6	NM_000600	90	CTGGATTCAATGAGGAGACTTGC	TCAAATCTGTTCTGGAGGTACTCTAGG
	IL-8	NM_000584	92	AAGACATACTCCAAACCTTTCCACC	CAATAATTTCTGTGTTGGCGCA
	TSLP	NM_033035	91	TCTTGTAGCAATCGGCCACA	ACATTTCTTTGGCGAGCGA
	TRAF1	NM_005658	91	TGGAAGATCACCAATGTCACCA	ATACTTGGCAGTGTAGAAGGCTGG
	TRAF3	NM_145752	91	GAAGGCGTGTAAATACCGGG	ACAGTCGGTGTCTTCGTGTTTCT
	NFKB2	NM_001077494	96	ACATGACTGCCCAATTTAACAACC	GGAGCCGCTGCCTCTGA
	IL-25	NM_022789	91	CACCCAGAGTCCTGTAGGGC	GGTTCAAGTCTCTGTCCAACTCATATC
	IL-33	NM_033439	51	AACACCCCTCAAATGAATCAGGT	TTGGCATGCAACCAGAAGTCT
Noncanonical; EMT	TNIP1	NM_001252385	92	ATCCAGTGGCACCTCCTCTG	CCAGCGCCATCGCATT
	SMA/ACTA2	NM_001141945	91	TGTAAGGCCGGCTTTGCT	TTCCCACCATCACCCCCT
	Col1A1	NM_000088	95	CCAGAAGAACTGGTACATCAGCA	CGCCATACTCGAACTGGAATC
	Vimentin	NM_003380	91	GCTCAATGTTAAGATGGCCCTT	TGGAAGAGGCAGAGAAATCCTG
	Desmin	NM_001927	91	GGAGAGGAGAGCCGGATCA	GGACCTCAGAACCCCTTTGC
	Twist1	NM_000474	101	TCTCGGTCTGGAGGATGGA	CAATGACATCTAGGTCTCCG
	Twist2	NM_001271893	119	ACGAGCGCCTCAGCTACG	CGCGACGGACAGCCCTG
	SLUG	AF084243	91	TGTGTGGACTACCGCTGCTC	ACTCACTCGCCCCAAAGATG
	SNAI1	NM_005985	95	GCGCTCTTTCCTCGTCAGG	GGGCTGCTGGAAGGTAAACTCT
	ITGA2	NM_002203	91	AGCCGAAGTACCAACAGGAGTTATA	GCCGAGCTTCCATAAAATTGC
	FSP1/S100A4	NM_002961	91	AGGGTGACAAGTTCAAGCTCAAC	GCTTCATCTGTCCTTTTCCCC
	SMA/ACTA2	NM_001141945	91	TGTAAGGCCGGCTTTGCT	TTCCCACCATCACCCCCT
IFN	IFNb	NM_002176	95	GCAGTTCCAGAAGGAGGACG	TCCAGCCAGTGCTAGATGAATC
	IFNa6	NM_021002	91	GTGGTGCTCAGCTGCAAGTC	CCAGGAGCATCATGGTCCTC
	IFNa21	NM_002175	91	TGATCTGCCTCAGACCCACA	CTTCAGGCAGGAGAAAGGAGAG
	CCL5/RANTES	NM_002985	96	TCTACACCAGTGGCAAGTGCTC	CCCGAACCCATTTCTTCTCTG
	DDX58/RIG1	NM_014314	132	CCACTTAAACCCAGAGACAATAACAA	TTGCCACGTCCAGTCAATATG
	LMP2	NM_002800	91	TTCACCACAGACGCTATTGCTC	CCACACCGGCAGCTGTAAT
	TAP1	NM_000593	91	GTTTTTCCAACAGAACCAGACAGG	GCTCAGATTCTCACTCAGAGAATCACT
	STAT1	NM_007315	104	TCCTGCTGCGGTTCAGTG	GGGTTCAACCGCATGGAAG
	STAT2	NM_005419	118	CCTGAAACACAGGCTCATTGTG	TGGCACCAGCCCTAGTTCC
	IRF1	NM_002198	91	AGCAAGGCCAAGAGGAAGTCA	TGCTGTGGTCATCAGGCAGA
	IRF9	NM_006084	91	AGCCACAGGAAGTTACAGACACAA	GCAGTGAGTAGTCTGGCTCTGGA
	SOCS3	NM_003955	91	CTTTCTGATCCGCGACAGCT	ACACTGGATGCGCAGGTTC
	IF127	NM_001130080	91	CAGTCACTGGGAGCAACTGGA	GCCCAGGATGAACTTGGTCA
	MX1	NM_001144925	106	GAACCACCCATATTTCAGGGATC	ATGTGTGATGAGCTCGCTGGTA
	IFNL1 (IL-29)	NM_172140	103	AAGCCCACCACAACTGGG	ACTCTTCCAAGGCGTCCC
	IFNL2 (IL-28A)	NM_172138	101	ACATGACTGGGGACTGCAC	ATCCGGGAGAGCCCCGT
	IFNL3 (IL-28B)	NM_172139	99	ATGACCGGGGACTGCATG	ATCCGGGAGAGCCCCGC
Growth factor	Fos	NM_005252	91	GGGCAAGGTGGAACAGTTATCT	GTTGCGGCATTTGGCTG
	c-Jun	NM_002228	91	GTCCCAGGAGCGGATCAAG	GGCGATTCTCTCCAGCTTCC
	SOD2	NM_000636	90	TGCTTGTCCAAATCAGGATCC	TGAAGGTAGTAAGCGTGCTCCC
	TM4SF1	NM_014220	91	GAGGTGGCCTGCTGATGCT	CCACAGTTTTCATGGCCACAG
ROS/DNA	NOX1	NM_007052	91	GGGCATCCCCCTGAGTCT	TCTGCTGGGAGCGGTAAAAC
	NOX4	NM_016931	91	ACTCAACACCCTGTTGGATGACT	CCAACGGAAGGACTGGATATCT
	HOXB9	NM_024017	91	GGCCGGATCAAACCAACC	TCCAGCGTCTGGTATTTGGTG
	ATM	NM_000051	127	GCTTCTCAGGATAATCCGCAAG	CCAAGCAGCTTCCAACAGC
	STK39 (SRT39)	NM_013233	91	GCCCAAAGAGCCAAAAAGGT	CGTCGTCACTCCACTCCCA
Cell cycle	PCNA	NM_002592	91	TGCGCCGGCAATGAA	CTTTCTCCTGGTTTGGTGCTTC
	CDKN1A	NM_000389	92	AGCAGGCTGAAGGGTCCC	GCGTTTGGAGTGGTAGAAATCTGT