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Notes
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
Mutant = ~200 bp
Heterozygote = ~200 bp and 280 bp
Wild type = 280 bp
>chr7:133557730-133558009 280bp GACTCCTCACCTGTCTCTTCTGA AGAGCTCCTCTTTACCTCCACA
Sequence
Wt Sequence:ATCGAGGTAACCAGTCAACACCCTTCCTGgagctgagccccgggtcCCCTGGCCTGGGATTGCACGTGGGGTCCCTGGGCATCTTGCTAGTGATTGTCAATGTCTCAGACCATATGGGGGGCT
Mutant Sequence: GACTCCTCACCTGTCTCTTCTGAGAAGCTGGCTTGGTATCGAGGTAACCAGTCAACACCCTTCCTGtagctgagcccccggtcgaccatgcccaagaagaagaggaaggTGTCCAATTTACTGACCGTACACCAAAATTTGCCTGCATTACCGGTCGATGCAACGAGTGATGAGGTTCGCAAGAACCTG
JAX Protocol
Protocol Primers
| Primer | 5' Label | Sequence 5' → 3' | 3' Label | Primer Type | Reaction | Note |
|---|---|---|---|---|---|---|
| 35897 | GAC TCC TCA CCT GTC TCT TCT GA | Common | A, B | |||
| 35898 | AGA GCT CCT CTT TAC CTC CAC A | Wild type Reverse | A | |||
| oIMR8990 | CAG GTT CTT GCG AAC CTC AT | Mutant Reverse | B |
Reaction A
| Component | Final Concentration |
|---|---|
| ddH2O | |
| Kapa 2G HS buffer | 1.30 X |
| MgCl2 | 2.60 mM |
| dNTPS-kapa | 0.26 mM |
| 35897 | 0.50 uM |
| 35898 | 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 |
| 35897 | 0.50 uM |
| oIMR8990 | 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
| Stock Number | Strain Name |
|---|---|
| 037070 | B6.129(C)-Cd19tm1(cre)Cgn Is(14)2Rdf/CjwuJ |
| 006785 | B6.129P2(C)-Cd19tm1(cre)Cgn/J |
| 027116 | B6.129P2-Cd19tm1(cre/ERT2)Rsky/J |
| 035514 | B6.Cg-Cd19tm1(cre)Cgn Ikzf3tm1.1Cjwu/J |
| 037632 | B6.Cg-Cd19tm1.1(cre)Cgn Rps15tm1.1Cjwu/J |
| 018958 | B6N.129P2-Cd19tm1(cre)Cgn/J |
| 004126 | C.Cg-Cd19tm1(cre)Cgn Ighb/J |
| 023806 | NOD.129P2(Cg)-Cd19tm1(cre)Cgn/J |
| 8 strains use this protocol | |