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Table 2 Oligonucleotides used in the present study.

From: Concurrent genotyping of Helicobacter pylorivirulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA

Primer

Primer sequence 5'-3' direction

PCR product (bp)

Gene/Region

Ref.d

pJB-1.SE

attcgatgcaacgcgaagaaccttacc

~430

16S rDNA

 

p13B.AS

gtgtactaggcccgggaacgtattc

 

(V3, V4, V9)

[38]

bio-HJ-HP-JBS.V3.SE

bio-cctaggcttgacattgaiagaa

~90

HP-16S rDNA

 

B-V3.AS

acgacagccatgcagcacct

 

pyrosequencing

 

vacA-1.SE

caatcgtgtgggttctggagc

678

vacA

 

vacA-3.AS

gccgatatgcaaatgagccgc

  

[15]

hsp60-1.SE

gctccaagcatcaccaaagacg

603

hsp60

 

hsp60-3.AS

gcggtttgccctctttcatgg

   

ureI-3.SE

cagcaatgggatttgcgggttaacca

511

ureI

 

ureI-4.AS

gatccaagcggttaaaataccctcaatgga

   

sod-1.SE

gccctgtggcgtttgatttcc

425

sodB

 

sod-3.AS

catgctcccacacatccacc

   

ureA-1.SE

gcggctgaattgatgcaagaagg

350

ureA

 

ureA-3M.SE

gctcgcaatgtctaagcgtttaccgaa

   

cagA-2.SE

gaaatttggggatcagcgttacc

180

cagA

 

cagA-3.AS

tcctgcaaaagattgtttggcaga

   

VAI-F

atggaaatacaacaaacacac

259/286

vacA s1/s2

 

VAI-R

ctgcttgaatgcgccaaac

  

[26]

VAG-F

caatctgtccaatcaagcgag

567/642

vacA m1/m2

 

VAG-R

gcgtcaaaataattccaagg

   

M13a-SeqS.SE

cgttgtaaaacgacggccagtga-ccctttgtgcaaaaatcgtt

381

vacA gene,

 

SeqS.AS

cccarcctccatcaatctt

 

signal region

 

M13a-SeqVac.SE

cgttgtaaaacgacggccagtga-gccaattcaayggcaattct

803

vacA RHM

pr.

SeqVac.AS

cgcttgattggacagattga

 

and i-region

 

M13a-SeqM.SE

cgttgtaaaacgacggccagtga-agtcrttgatgggccttttg

717b

vacA gene, midregion

 

IL1B-511F1.SE

tatgttctctgccccagcca

133

IL1B-511

 

bio-IL1B-511R1.AS

bio-aatagccctccctgtctgtattga

 

rs16944c

pr.

Seq-IL1B-511.S1

gcaattgacagagagct

 

pyrosequencing

 

bio-IL1B-31F1.SE

bio-atttctcagcctcctacttctgc

76

IL1B-31

 

IL1B-31R1.AS

aagaggtttggtatctgccagttt

 

rs1143627c

pr.

Seq-IL1B-31.S1

ccctcgctgtttttat

 

pyrosequencing

 

hIL1B+3954.AS

cggagcgtgcagttcagtgat

152

IL1B +3954

 

bio-IL1B+3954.SE

bio-aattttgccgcctcgcctca

 

rs1143634c

[27]

IL1B+3954

cgttatcccatgtgtc

 

pyrosequencing

 

IFNGR1.SE

ggtgacggaagtgacgtaagg

106

IFNGR1-56

 

bio-IFNGR1.AS

gaggagagccatgctgctac

 

rs2234711c

pr.

Seq-IFNGR1.S2

gccggggctggaggg

 

pyrosequencing

 

IL1RNF1.SE

cccctcagcaacactcc

270/356/442

IL1RN 86bp

[17]

IL1RNR1.AS

ggtcagaagggcagaga

/528/614

VNTR/Intron 2

 
  1. a) underlined sequence corresponds to a M13-sequence adapter used in DNA sequencing.
  2. b) expected PCR product using M13-SeqM.SE and VAG-R primers.
  3. c) rs: Reference SNP identification number [58]
  4. d) pr. – present study.
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BMC Microbiology

ISSN: 1471-2180

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