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Chunk #7 — Materials and Methods — Simple Sequence Repeat Genotyping

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Fine mapping of calcineurin (PPP3CA) gene reveals novel alternative splicing patterns, association of 5'UTR trinucleotide repeat with addiction vulnerability, and differential isoform expression in Alzheimer's disease.
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SSLPs were genotyped using PCR amplifications in which one primer of the pair was labeled with carboxylfluorescein (6-FAM) at the 5′-terminal end of the primer (Table S1). For the PPP3CA_Prmt and PPP3CA_Int2 primer pairs, genomic DNA samples (10 ng/μl) were added to the reaction using 1× Gold buffer, 1.5 mM MgCl2, 0.8 mM dNTPs, 20 μM of each oligonucleotide primer, and 0.13 U of AmpliTaq Gold polymerase. Each 5 μl reaction used a procedure of 94°C for 5 min, 35 cycles of 94°C for 0.5 min, 55°C for 0.5 min, 72°C for 0.75 min, followed by 72°C for 7 min. The PPP3CA_EX1 primer pair required use of Herculase Hotstart DNA polymerase (Stratagene, La Jolla, CA) and 5% dimethylsulfoxide (DMSO) to amplify this GC-rich region. For the 5 μl reaction, genomic DNA samples were amplified using a procedure of 95°C for 10 min, 45 cycles of 94°C for 0.5 min, 62°C for 0.5 min, 72°C for 0.75 min, followed by 72°C for 10 min. The PCR products were denatured with Hi-Di Formamide (Applied Biosystems, Foster City, CA) at 95° for 5