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Table 3 Nucleotide primers used in multiplex PCR and m-FISH probes

From: Development of multiplex PCR and multi-color fluorescent in situ hybridization (m-FISH) coupled protocol for detection and imaging of multi-pathogens involved in inflammatory bowel disease

Bacterial gene target nPCR primers Multiplex PCR primers m-FISH probe
Mycobacterium avium subspecies paratuberculosis
(MAP)
IS900
P90: 5′-GTTCGGGGCCGTCGCTTAGG-3′
(BLAST E-value: 2e−04)
P91: 5′-GAGGTCGATCGCCCACGTGA-3′
(BLAST E-value: 2e−04)
AV1: 5′-ATGTGGTTGCTGTGTTGGATGG-3′
(BLAST E-value: 1e−05)
AV2: 5′-CCGCCGCAATCAACTCCAG-3′
(BLAST E-value: 5e−04)
AV1: 5′-ATGTGGTTGCTGTGTTGGATGG-3′
(BLAST E-value: 1e−05)
AV2: 5′-CCGCCGCAATCAACTCCAG-3′
(BLAST E-value: 5e−04)
AV1: 5′-AF488 ATGTGGTTGCTGTGTTGGATGG-3′
(BLAST E-value: 1e−05)
Mycobacterium avium complex
(MAC)
IS1311
NA Forward: 5′-AAACGACCAAGGATCACTACCGAG-3′
(BLAST E-value: 1e−06)
Reverse: 5′-GTCGAGGAACACATACGGGAAGT-3′
(BLAST E-value: 4e−06)
NA
Non-pathogenic E. coli strain K-12
18s
NA Forward: 5′-CCGCATAACGTCGCAAGACC-3′
(BLAST E-value: 6e−04)
Reverse: 5′-CGTAGGAGTCTGGACCGTGTC-3′
(BLAST E-value: 2e−04)
5′-AF647 GGTCTTGCGACGTTATGCGG-3′
(BLAST E-value: 6e−04)
AIEC strain LF82
gipA
NA Forward: 5′-GCTGTGTGCGCTTCGTCTAC-3′
(BLAST E-value: 4e−08)
Reverse: 5′-GATGGTAATTCTCGACTCCAGCGA-3′
(BLAST E-value: 2e−07)
5′-AF568 GTAGACGAAGCGCACACAGC-3′
(BLAST E-value: 4e−08)
K. pneumoniae
23 s
NA Forward: 5′-TGGCAGTCAGAGGCGATGAAG-3′
(BLAST E-value: 1e−04)
Reverse: 5′-CTTTCCCTCACGGTACTGGTTCA-3′
(BLAST E-value: 0.002)
5′-AF546 CTTCATCGCCTCTGACTGCCA-3′
(BLAST E-value: 0.001)
  1. BLAST E-value: basic local alignment search tool expected value