Table 1

DNA oligonucleotides used in this study

Probe nameaSequenceb
Pre16S 15 m 48D5′-TTTTTCGTCTTGCGA-F
Pre16S 15 m 63C5′-B-GAGACTTGGTATTCA
Pre16S 15 m R63D5′-F-GAGACTTGGTATTCA
Pre16S 15 m R48C5′-TTTTTCGTCTTGCGA-B
Pre16S 17 m R63D5′-F-TTGAGACTTGGTATTCA
Pre16S 17 m R46C5′-TTTTTCGTCTTGCGACG-B
Pre16S 19 m R63D5′-F-TCTTGAGACTTGGTATTCA
Pre16S 19 m R44C5′-TTTTTCGTCTTGCGACGTT-B
Pre16S 21 m R63D5′-F-ACTCTTGAGACTTGGTATTCA
Pre16S 21 m R42C5′-TTTTTCGTCTTGCGACGTTAA-B
Pre16S 17 m R60D5′-F-AGACTTGGTATTCATTT
Pre16S 17 m R43C5′-TTCGTCTTGCGACGTTA-B
Pre16S 19 m R60D5′-F-TGAGACTTGGTATTCATTT
Pre16S 19 m R41C5′-TTCGTCTTGCGACGTTAAG-B
Pre16S 21 m R60D5′-F-CTTGAGACTTGGTATTCATTT
Pre16S 21 m R39C5′-TTCGTCTTGCGACGTTAAGAA-B
Pre16S 17 m R66D5′-F-CTCTTGAGACTTGGTAT
Pre16S 17 m R49C5′-TCATTTTTCGTCTTGCG-B
Pre16S 19 m R66D5′-F-CACTCTTGAGACTTGGTAT
Pre16S 19 m R47C5′-TCATTTTTCGTCTTGCGAC-B
Pre16S 21 m R66D5′-F-TTCACTCTTGAGACTTGGTAT
Pre16S 21 m R45C5′-TCATTTTTCGTCTTGCGACGT-B
Pre16S 19 m 5′JxnD5′-TTTGATGCTCAAAGAATTA-F
Pre16S 21 m 5′JxnC5-S-TCAAACTCTTCAATTTAAAAG
Pre16S 21 m R5′JxnD5-F-TCAAACTCTTCAATTTAAAAG
Pre16S 19 m R5′JxnC5′-TTTGATGCTCAAAGAATTA-S
Pre16S 17 m 3′JxnD5′-GAGGTGATCCAACCGCA-F
Pre16S 20 m 3′JxnC5-S-GAACGCTTCTTTAAGGTAAG
Pre16S 20 m R3′JxnD5-F-GAACGCTTCTTTAAGGTAAG
Pre16S 17 m R3′JxnC5′-GAGGTGATCCAACCGCA-S
Pre23S 17 m 3′JxnDc5′-AAGCCTCACGGTTCATT-F
Pre23S 14 m 3′JxnCc5′-S-GGCGTTGTAAGGTT
Pre23S 14 m R3′JxnD5′-F-GGCGTTGTAAGGTT
Pre23S 17 m R3′JxnC5′-AAGCCTCACGGTTCATT-S
Mature rRNA 18 m 1484D5′-GTTACGACTTCACCCCAG-F
Mature rRNA 19 m 1502C5′-S-GTTCCCCTACGGTTACCTT
Synthetic target oligonucleotides
Pre-rRNA 31 m5′-AATGAACCGTGAGGCTTAACCTTACAACGCC
Mature rRNA 37 m5′-CTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAAC
  • a m, number of nucleotides; C, capture probe; D, detector probe; Jxn, splice site; R, reverse orientation.

  • b F, FITC; B, biotin; S, thiol.

  • c Capture and detector probe pair selected based on its high signal-to-noise ratio.