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Stock No: 008873
Protocol 28361: Separated PCR Assay - Gli3<tm1Alj>
Version 2.2
Notes
This assay does not work well without the use of a Hotstart.
When using the two primers flanking the loxp sites (Reaction A), the assay may not reliably amplify both fragments from heterozygous mutant mice. Therefore we have included a mutant specific (loxp) primer that can be used to amplify from the mutant allele (Recation B).
When using the two primers flanking the loxp sites (Reaction A), the assay may not reliably amplify both fragments from heterozygous mutant mice. Therefore we have included a mutant specific (loxp) primer that can be used to amplify from the mutant allele (Recation B).
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
Reaction A (8920 and 8921):
Mutant = ~500 bp
Heterozygote =~500bp, and 195 bp
Wild type = 195bp
Reaction B (8921 and oIMR9042):
Mutant = ~ 350 bp
Wild type = no amplification
Mutant = ~500 bp
Heterozygote =~500bp, and 195 bp
Wild type = 195bp
Reaction B (8921 and oIMR9042):
Mutant = ~ 350 bp
Wild type = no amplification
JAX Protocol
Protocol Primers
| Primer | 5' Label | Sequence 5' → 3' | 3' Label | Primer Type | Reaction | Note |
|---|---|---|---|---|---|---|
| 8920 | CTG GAT GAA CCA AGC TTT CCA TC | A | ||||
| 8921 | CTG CTC AGT GCT CTG GGC TCC | A, B | ||||
| oIMR9042 | CTT CGT ATA GCA TAC ATT ATA CG | B |
Reaction A
| Component | Final Concentration |
|---|---|
| ddH2O | |
| Kapa 2G HS buffer | 1.30 X |
| MgCl2 | 2.60 mM |
| dNTPS-kapa | 0.26 mM |
| 8920 | 0.50 uM |
| 8921 | 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.
Reaction B
| Component | Final Concentration |
|---|---|
| ddH2O | |
| Kapa 2G HS buffer | 1.30 X |
| MgCl2 | 2.60 mM |
| dNTPS-kapa | 0.26 mM |
| 8921 | 0.50 uM |
| oIMR9042 | 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.