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Table 1 Target for probes and sequences of rRNA-targeting oligonucleotide probes and 16S rRNA gene targeting primers used in this study

From: Community analysis of bacteria colonizing intestinal tissue of neonates with necrotizing enterocolitis

Targets for probes Oligonucleotide Probes Sequence Fluorophor Reference
Bacteria S-D-bact-0338-a-A-18 5' GCT GCC TCC CGT AGG AGT 3' Fluorescein [37]
Enterobateria GAM42a 5' GCC TTC CCA C(AT)TCGT TT 3' Fluorescein [38]
  S-S-C.perfring-185-a-A-18 5'TGG TTG AAT GAT GAT GCC 3' Cy3 [21]
Clostridium spp. 1 S-S-C.paraputri-181 5' CAT GCG AAC GTA CAA TCT 3' Cy3 This study
  S-S-C. butyricum-663 5'AGG AAT TCT CCT TTC CTC 3' Cy3 This study
  S-S-C.diff-193-a-A-18 5'TGT ACT GGC TCA CCT TTG 3' Cy3 [21]
Actinobacteria pB-00182 5'TA TAG TTA CCA CCG CCG T 3' Cy3 [39]
Lactobacillus & Enterococcus Lab158 5'GGTAT TAJ CAY CTG TTTCCA3' Cy3 [40]
Bifidobateria pB-00037 5'CC AGT GGC TAT CCC TGT GTG AAG G3' Cy3 [41]
  PCR Primers    
Bacteria Bact64f 5'-CY TAA YRC ATG CAA GTC G-3'   [42]
Bacteria Bact109r1 5'-YY CAC GYG TTA CKC ACC CGT-3'   [42]
Bacteria PyroBact64f 5'-CAT GCA AGT CG-3' Biotin C-6 This study
  1. 1 The Clostridium probe is a mixture of four clostridium species: C. perfringens, C. difficile, C. butyricum and C. parputrificum