Talk:20.109(S13):Context-setting and primer design (Day1): Difference between revisions
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| Line 126: | Line 126: | ||
|5' CCA GGT TGA TTC TGC CTG 3' | |5' CCA GGT TGA TTC TGC CTG 3' | ||
|5' CTC TCC GGA ACC AAA CC 3' | |5' CTC TCC GGA ACC AAA CC 3' | ||
|bp | |bp 9 | ||
|bp | |bp 225 | ||
| | |VC, SSU, rRNA | ||
|- | |- | ||
|Platinum | |Platinum | ||
Revision as of 14:23, 13 February 2013
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 | 5' GGA CGG CTC AGT GAT AG 3' | ||||
| Yellow | 5' GAGAAGTAAGATGTTTAGCAAGTAT 3' | 5' CATCACCACAAAAGTCCAA 3' | bp 359, F | bp 630, R | EH, SSU rRNA |
| Red | 5' CCA GGT TGA TTC TGC CTG 3' | 5' CTC TCC GGA ACC AAA CC 3' | bp 9 | bp 225 | VC, SSU, rRNA |
| Platinum | 5' CAT GTT GAT TCT GCC TGA C 3' | 5' CTC TCC TGA ACC AAA CCC TG 3' | bp 4, F | bp 278, R | EH, SSU rRNA |
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 | ACGAGCAATACAGGAGTGG | TCCATCTGAGCACCTTCC | bp 841 | bp 1049 | VC SSU rRNA |
