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Notes
Taqman qPCR protocols are run on a real time PCR instrument. Use an appropriate instrument specific Fluorophore/Quencher combination. The transgene genotype is determined by comparing ΔCt values of each unknown sample against known homozygous and hemizygous controls, using appropriate endogenous references.
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
Mut= 103 bp
Wt= 105 bp
Sequence
Sequence (deletion in lower case):
AATCAGAGGCTTTCCCATGTGATAATGAAGTGTTTAATCACcataatgttatggagaaacagcatttaatgtttggctaaaccttctttctttatcttttcagataaattattagtcataactgtcgcaacaaaagaaaatgatggattccacagatttatgaattcagccaagtatttcaattacactgtgaaggtatgatatgtctttcagtctttggacttgttggaatatgtgcctaaaatatattaactagtggtttatttaaacatgttctataagcaacagaaatgtgtatatatgtaactttcctgacttcctttggagggtcatgtccacatacattgtaatcaaggtttgacggtaactattttcactgactaaagggatggcctgctgtggtgtcagttgaaaacatgatgggacggggcTTTGGGGGTGCGCTATTGACAGTGTTTTTCCTGTTTTGTTTGGTTTGGGTTCATTGGTTGGA
JAX Protocol
Protocol Primers
| Primer | 5' Label | Sequence 5' → 3' | 3' Label | Primer Type | Reaction | Note |
|---|---|---|---|---|---|---|
| 34387 | AAT CAG AGG CTT TCC CAT GT | Common | A | |||
| 34388 | Fluorophore-1 | TGG AGA AAC AGC ATT TAA TGT TTG G | Quencher-1 | WT Probe | ||
| 34389 | ATC TGA AAA GAT AAA GAA AGA AGG TTT | Wild type Reverse | A | |||
| 34390 | TCC AAC CAA TGA ACC CAA AC | Mutant Reverse | A | |||
| 34391 | Fluorophore-2 | TGC GCT ATT GAC AGT GTT TTT C | Quencher-2 | MUT Probe |
Reaction A
| Component | Final Concentration |
|---|---|
| Kapa Probe Fast QPCR | 1.00 X |
| ddH2O | |
| 34387 | 0.40 uM |
| 34389 | 0.40 uM |
| 34390 | 0.40 uM |
| Wt Probe | 0.15 uM |
| Mutant Probe | 0.15 uM |
| DNA |
Cycling
| Step | Temp °C | Time | Note |
|---|---|---|---|
| 1 | 95.0 | -- | |
| 2 | 95.0 | -- | |
| 3 | 60.0 | -- | |
| 4 | -- | repeat steps 2-3 for 40 cycles | |
| 5 | 40.0 | -- | Forever |
JAX uses a very high speed Taq (~1000 bp/sec), use cycling times recommended for your reagents.
Strains Using This Protocol
This is the only strain that uses this protocol.