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Table 1 Sequences of primers and probes used in real-time RT-PCR analysis

From: Substitution of dietary fish oil with plant oils is associated with shortened mid intestinal folds in Atlantic salmon (Salmo salar)

Gene Gene Sequence 5′ → 3′ GenBank accession no. Pyloric caeca Mid intestine Distal intestine
EF1AB F-TGCCCCTCCAGGATGTCTAC BG933853 18.19 ± 0.09 19.74 ± 0.28 18.90 ± 0.15
R-CACGGCCCACAGGTACTG
P-FAM-AAATCGGCGGTATTGG-MGB
CD3ζ F-AACAGGGATCCAGAGAGTGCTG BT060238 27.77 ± 0.16 27.74 ± 0.28 27.41 ± 0.20
R-AAGGGACGTGTAAGTGTCGTCA
P-FAM-ACGGCACGCGATAATCGCAGGA-BHQ
COX-2a F-CAGATCGCTGGAAGGGTGG AY848944 33.66 ± 0.31 33.32 ± 0.43 32.83 ± 0.35
R-TCATGTTGAAGCGTTTCCTGTAG     
P-FAM-AGCTAAGGCCCTGGAGCACAGC-BHQ
IgM F-TGTAAAGAGAGCAGACTGGGACAG Y12456 25.60 ± 0.55 24.89 ± 0.60 24.63 ± 0.45
R-GAGACGGGTGCTGCAGATATTC Y12457
P-FAM-TGTTCCACGGCGCATTCAAAGATTT-BHQ
IgT F-CAGCAGTCTGCTGAAGGTC GQ907004 29.91 ± 0.29 30.29 ± 0.50 28.00 ± 0.30
R-GGTTCTGTTTTGGAGATCG GQ907003
P-FAM-CTGCACCACACAGCTGTACTTGACC-BHQ
IL-1β F-GCTACCACAAAGTGCATTTG AY617117 34.91 ± 0.42 33.91 ± 0.64 31.98 ± 0.33
R-GAGGTTGGATCCCTTTATGC
P-FAM-CCATTGAGACTAAAGCCAGACCTGTAG-BHQ
MHCII F-CCACCTGGAGTACACACCCAG X70165 20.95 ± 0.25 20.34 ± 0.35 20.49 ± 0.18
R-TTCCTCTCAGCCTCAGGCAG
P-FAM-TCCTGCATGGTGGAGCACATCAGC-BHQ
NOD2 F-GCATCCAGTGTGAGCACTTTCAG EG915470 32.01 ± 0.19 31.55 ± 0.24 31.86 ± 0.23
R-TTCATCTTCAGGAGGTGAGCG
P-FAM-CAAGCTAACTGATGCCTGCACAGAGTGC-BHQ
TGF-β F-TGGAGCTGAGTGAGGAGCAG EU082211 34.04 ± 0.29 34.24 ± 0.41 33.46 ± 0.32
R-ACCGCATCTCAGACATGTTG
P-FAM-TGTGGACCTCCTTTGCAAAGTATGC-BHQ
TNF-α F-GCAGCTTTATGTGCGGCAG NM_001123589 36.38 ± 0.30 NA 35.47 ± 0.29
R-TTTTGCACCAATGAGTATCTCCAG NM_001123590
P-FAM-TGGAAGACTGGCAACGATGCAGGA-BHQ
  1. The mean Ct-values ± SEM for the fish oil group are given for each intestinal segment.
  2. NA, Not applied.