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Stock No: 001162
Protocol 28929: Sanger sequencing Assay - H2-Ab1<bm12>-SEQ
Version 1.2
Notes
Mut = T A A
WT= A G C
The genotyping protocol(s) presented here have been optimized for reagents and conditions used by The Jackson Laboratory (JAX).
To genotype animals, JAX recommends researchers validate the assay independently upon receipt of animals into their facility.
Reaction cycling temperature and times may require additional optimization based on the specific genotyping reagents used.
Expected Results
Sequence
AGTGCTACTTCACCAACGGGACGCAGCGCATACGATATGTGACCAGATACATCTACAACCGGGAGGAGTA
CGTGCGCTACGACAGCGACGTGGGCGAGCACCGCGCGGTGACCGAGCTGGGGCGGCCAGACGCCGAGTAC
TGGAACAGCCAGCCGGAG(a/t)TCCTGGAGC(g/a)AA(c/a)GCGGGCCGAGCTGGACACGGTGTGCAGACACAACTACG
AGGGGCCGGAGACCCACACCTCCCTGCGGCGGCTTGGTGAGCGCGGCGGGTCCCGCGGGAGCGCGGCGGG
CCGTGAGGGGACGCGGAGCAGAGTTCCCGCCTGAGGAGCTGCATGGCCTCCTTCCTCCCGTCTGCCCTGC
JAX Protocol
Protocol Primers
| Primer | 5' Label | Sequence 5' → 3' | 3' Label | Primer Type | Reaction | Note |
|---|---|---|---|---|---|---|
| 24439 | GAG TAC GTG CGC TAC GAC AG | Forward | A | |||
| oIMR5239 | AGG GAG GTG TGG GTC TCC | Reverse | A |
Reaction A
| Component | Final Concentration |
|---|---|
| ddH2O | |
| Kapa 2G HS buffer | 1.30 X |
| MgCl2 | 2.60 mM |
| dNTPS-kapa | 0.26 mM |
| 24439 | 0.50 uM |
| oIMR5239 | 0.50 uM |
| Glycerol | 6.50 % |
| Dye | 1.00 X |
| Kapa 2G HS taq polym | 0.03 U/ul |
| DNA |
Cycling
| Step | Temp °C | Time | Note |
|---|---|---|---|
| 1 | 94.0 | -- | |
| 2 | 94.0 | -- | |
| 3 | 65.0 | -- | -0.5 C per cycle decrease |
| 4 | 68.0 | -- | |
| 5 | -- | repeat steps 2-4 for 10 cycles (Touchdown) | |
| 6 | 94.0 | -- | |
| 7 | 60.0 | -- | |
| 8 | 72.0 | -- | |
| 9 | -- | repeat steps 6-8 for 28 cycles | |
| 10 | 72.0 | -- | |
| 11 | 10.0 | -- | hold |
JAX uses a very high speed Taq (~1000 bp/sec), use cycling times recommended for your reagents.
JAX uses a 'touchdown' cycling protocol and therefore has not calculated the optimal annealing temperature for each set of primers.
Strains Using This Protocol
This is the only strain that uses this protocol.