Talk:20.109(S13):Context-setting and primer design (Day1)
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|bp 18 | |bp 18 | ||
|bp 199 | |bp 199 | ||
| - | |VC | + | |VC small subunit ribosomal RNA gene |
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| Line 60: | Line 60: | ||
|- | |- | ||
| Purple | | Purple | ||
| - | | | + | |5' AGC CGC GGT AAT ACC GAC 3' |
| - | | | + | |5’ GA TTT CTC CCT GCC CAC TGT 3’ |
| - | | | + | | bp 385, F |
| - | | | + | | bp 699, R |
| - | | | + | |VC, SSU rRNA |
|- | |- | ||
|Red | |Red | ||
| Line 109: | Line 109: | ||
|Is bp # for VC or EH? Which gene? | |Is bp # for VC or EH? Which gene? | ||
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| - | | | + | |Purple |
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| - | | | + | |Yellow |
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| - | | | + | |Red |
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| - | | | + | |Platinum |
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| Line 150: | Line 150: | ||
|Target side (e.g., bp 300), R | |Target side (e.g., bp 300), R | ||
|Is bp # for VC or EH? Which gene? | |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 | | Blue | ||
| TBA | | TBA | ||
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| TBA | | TBA | ||
| TBA | | TBA | ||
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Revision as of 00:07, 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) :) | CCA TGC TTG CCA ACA CAG G | GGT CTG GTT GCT TCC ACT TCC | bp 8 | bp 227 | E. Hellem: polar tube protein gene |
| Green | |||||
| Pink | |||||
| 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' AGC CGC GGT AAT ACC GAC 3' | 5’ GA TTT CTC CCT GCC CAC TGT 3’ | bp 385, F | bp 699, R | VC, SSU rRNA |
| Red | |||||
| Orange | |||||
| 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 |
