Daniel:Notebook/PosSequencing/Oligos
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Oligonucleotides[edit]
Components:
Component | Sequence | Reverse Complement | Length | Tm (C, 0.5 uM Primer concentration) |
Adapter 0 | CCTCATGCGTATCCGAT | ATCGGATACGCATGAGG | 17 | 53.54 |
Adapter 1 (Primer2) | AACAGTGCTCTTCCAGTCTA | TAGACTGGAAGAGCACTGTT | 20 | 50.94 |
Add PolydT | NBAAAAAAAAAAAAAAAAAAAATAGACTGGAAGAGCACTGTT | AACAGTGCTCTTCCAGTCTATTTTTTTTTTTTTTTTTTTTVN | 42 | 53.9 |
dcProbe6-488 (barcode 1) | CACGCTTACGATCCCGCTAT | ATAGCGGGATCGTAAGCGTG | 20 | 60.93 |
dcProbe6-Cy3 (barcode 2) | TCGTAACCCGTGCGAAGTGC | GCACTTCGCACGGGTTACGA | 20 | 65.15 |
dcProbe6-Cy5 (barcode 3) | CTCTCGTAGCGTGCGATGAG | CTCATCGCACGCTACGAGAG | 20 | 60.68 |
- Note: From this paper the working formula for adding formamide is -0.58 +/- 0.05 C/% FA. According to this a 25% formamide solution will affect Tm by 14.7C give or take 1C.
Biotin Uracil Primer 1
5-/5BiotinTEG/CAGTGTUCCTCATGCGTATCCGAT-3
Biotin EcoRI Primer 1
5-/5BiotinTEG/GGAATTCCCCTCATGCGTATCCGAT-3
BarcodeOligov1 (dcProbe6-488)
5TAGACTGGAAGAGCACTGTTCATCATCAT-GGGTAGTGTGTAGGAATTCC-CACGCTTACGATCCCGCTAT-ATCGGATACGCATGAGG3
BarcodeOligov2 (dcProbe6-Cy3)
5TAGACTGGAAGAGCACTGTTCGATGTACG-GGGTAGTGTGTAGGAATTCC-TCGTAACCCGTGCGAAGTGC-ATCGGATACGCATGAGG3
BarcodeOligov3 (dcProbe6-Cy5)
5TAGACTGGAAGAGCACTGTTGGACTTGAA-GGGTAGTGTGTAGGAATTCC-CTCTCGTAGCGTGCGATGAG-ATCGGATACGCATGAGG3