Talk:20.109(S13):Context-setting and primer design (Day1)
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| - | | | + | |AGG TTG ATT CTG CCT GAC |
| - | + | |CGG AAC CAA ACC CTG AT | |
| - | | | + | |bp 5 |
| - | | | + | |bp 236 |
| - | | | + | |VC: SSU rRNA |
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Revision as of 17:22, 12 February 2013
Contents |
T/R section
Please sign up for one of the design challenges -- four teams per challenge -- right away.
When you have finished, post your primer sequences (from 5' to 3') so that they can be ordered.
I will name your primers by the approximate base-pair that they target in V corneae or E hellem, so please share this information as well.
Sensitivity
| Team color | Forward (F) primer | Reverse (R) primer | Target site (e.g. bp 60), F | Target side (e.g., bp 300), R | Is bp # for VC or EH? Which gene? |
| Grey (Platinum) :) | CAT GCT TGC CAA CAC AG | GAA TGG TCT GGT TGC TTC | bp 9 | bp 251 | E. Hellem: polar tube protein gene |
| Green | AGG TTG ATT CTG CCT GAC | CGG AAC CAA ACC CTG AT | bp 5 | bp 236 | VC: SSU rRNA |
| Pink | ttctgcctgacgtagatg | cctctccggaaccaaac | bp 12 | bp 226 | VC |
| Yellow | CTGACGTGGATGCTATTC | CCGTCAACCGTCACTGTC | bp 18 | bp 199 | VC small subunit ribosomal RNA gene |
Specificity
| Team Color | Forward primer | Reverse primer | Target site (e.g. bp 60), F | Target side (e.g., bp 300), R | Is bp # for VC or EH? Which gene? |
| Purple | 5' GCG ATG ATT TAG TCT GGC 3' | 5’ CAA TTT CCA ACG ACC ATG C 3’ | bp 93, F | bp 879, R | VC, SSU rRNA |
| Red | GGT TGA TTC TGC CTG ACG TGG | CCT TCG TCC TTC ATC ACC ACA A | bp 6, F | bp 588, R | VC, SSU RNA |
| Orange | 5'cgt agt cat aga agg gca aag ag3' | 5' ctc tct ctc tac ctg cta ttg ta 3' | 441 | 1005 | V. corneae TV4/TV5 SSU rRNA |
| Blue | CCGCAATCAGGGACGAA | GTCAACGTCACTGTCTTGG | 60 | 195 | V. corneae TV4/TV5 SSU rRNA |
W/F section
Please sign up for one of the design challenges -- four teams per challenge -- right away.
When you have finished, post your primer sequences (from 5' to 3') so that they can be ordered.
I will name your primers by the approximate base-pair that they target in V corneae or E hellem, so please share this information as well.
Sensitivity
| Team color | Forward (F) primer | Reverse (R) primer | Target site (e.g. bp 60), F | Target side (e.g., bp 300), R | Is bp # for VC or EH? Which gene? |
| Purple | |||||
| Yellow | |||||
| Red | |||||
| Platinum |
Specificity
| Team Color | Forward primer | Reverse primer | Target site (e.g. bp 60), F | Target side (e.g., bp 300), R | Is bp # for VC or EH? Which gene? |
| Pink | TTCTGCCTGACGTAGATG | TCAACCGTCACTGTCTTG | bp 12 | bp 213 | for VC TV4 SSU rRNA |
| Green | AATCAGGGACGAATAGCTC | TGATAGTCCTGCGTCTTATTC | bp 64 | bp 169 | VC SSU rRNA, full sequence |
| Orange | CTGCCTGACGTAGATGCTAG | CTGTCTTGGTAGTCCACTAC | bp 14 | bp 203 | VC TV4 SSU rRNA gene |
| Blue | TBA | TBA | TBA | TBA | TBA |
