Research Article
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 |
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