Stock Number:005654
Strain Name:B6C3-Del(16Cbr1-ORF9)1Rhr/J
Del(16Cbr1-ORF9)1Rhr
Del(16Cbr1-ORF9)1Rhr
Separated PCR
1.1
08-July -2008 16-August -2010
Expected Results: Mutant = ~350 bp
Heterozygote = 200 bp and ~350 bp
Wild type = 200 bp
Gel Information: Separated by gel electrophoresis on a 1.5% agarose gel.
Protocol Primers 
Primer 5' Label Sequence 5' --> 3' 3' Label Primer Type
oIMR3995 - CTC GTC CTG CAG TTC ATT CA - Mutant
oIMR4003 - GGA CGG TTG GAG AAG AAG GT - Mutant
oIMR8744 - CAA ATG TTG CTT GTC TGG TG - Internal Positive Control Forward
oIMR8745 - GTC AGT CGA GTG CAC AGT TT - Internal Positive Control Reverse
Reaction/Components 
Reaction Component Volume (µl) Final
Concentration		 Total Volume (µl)
ddH2O 3.96 - 3.96
10 X AB PCR BufferII 1.20 1.00 X 1.20
25 mM MgCl2 0.96 2.00 mM 0.96
2.5 mM dNTP 0.96 0.20 mM 0.96
20 uM oIMR3995 0.60 1.00 uM 0.60
20 uM oIMR4003 0.60 1.00 uM 0.60
5 mM DNA Loading Dye 1.66 0.69 mM 1.66
5 U/ul Taq DNA Polymerase 0.06 0.03 U/ul 0.06
DNA 2.00 - 2.00
Cycling 
Step # Temp °C Time Note
1 94 3 min -
2 94 30 sec -
3 65 1 min -
4 72 1 min repeat steps 2-4 for 35 cycles
5 72 2 min -
6 10 - hold
Reaction/Components 
Reaction Component Volume (µl) Final
Concentration		 Total Volume (µl)
ddH2O 3.96 - 3.96
10 X AB PCR BufferII 1.20 1.00 X 1.20
25 mM MgCl2 0.96 2.00 mM 0.96
2.5 mM dNTP 0.96 0.20 mM 0.96
20 ul oIMR8744 0.60 1.00 ul 0.60
20 uM oIMR8745 0.60 1.00 uM 0.60
5 mM DNA Loading Dye 1.66 0.69 mM 1.66
5 U/ul Taq DNA Polymerase 0.06 0.03 U/ul 0.06
DNA 2.00 - 2.00
This genotyping protocol is used for the following strains:
 
Stock Number Strain Name
005654 B6C3-Del(16Cbr1-ORF9)1Rhr/J
Genotyping resources and troubleshooting
This page contains guidelines, frequently asked questions, and helpful external links to genotyping and PCR resources.
Cycling 
Step # Temp °C Time Note
1 94 3 min -
2 94 30 sec -
3 65 1 min -
4 72 1 min repeat steps 2-4 for 35 cycles
5 72 2 min -
6 10 - hold