Yeast DNA Prep protocol - source code
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<code> #include "BioCoder.h" void main() { start_protocol("Yeast DNA Prep"); Fluid yeast_cul = new_fluid("yeast culture grown up to appropriate density", "near saturation"); Fluid break_buffer = new_fluid("breaking buffer", "2% (v/v) Triton X-100, 1% (w/v) SDS, 100 mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA, pH 8.0"); Fluid phe_chloro_iaa = new_fluid("phenol : chloroform : isoamyl alcohol", "25:24:1", ICE_COLD); Fluid te = new_fluid("TE buffer", "10 mM Tris-Cl, pH 8.0, 1 mM EDTA, pH 8.0"); Fluid ethanol = new_fluid("95% ethanol", ICE_COLD); Fluid water = new_fluid("water"); Solid glass_beads = new_solid("glass beads"); Container eppendorf1 = new_container(EPPENDORF); Container eppendorf2 = new_container(EPPENDORF); Container eppendorf3 = new_container(EPPENDORF); //1. grow up yeast culture to appropriate density (near saturation) //2. spin 1.5 mls of culture for 1 min in microfuge and aspirate off supernatant first_step(); measure_fluid(yeast_cul, vol(1.5, ML), eppendorf1); centrifuge_pellet(eppendorf1, speed(SPEED_MAX, RPM), RT, time(1, MINS)); //3. resuspend pellet in 200 ul breaking buffer next_step(); measure_and_add(eppendorf1, break_buffer, vol(200, UL)); resuspend(eppendorf1); //4. wear gloves and add: // * 200 ul phenol:choloroform:isoamyl alcohol (25:24:1) // * 200 ul (@200 mg) glass beads next_step(); measure_and_add(eppendorf1, phe_chloro_iaa, vol(200, UL)); measure_and_add(eppendorf1, glass_beads, 200, MG); comment("Wear gloves for this step!"); //5. close cap tightly and vortex for 2.5 min. // * Be careful when vortexing; label can be dissolved by the phenol. // * Hold cap tightly so it doesn't open or spill. next_step(); vortex(eppendorf1, time(2.5, MINS)); comment("Be careful when vortexing; label can be dissolved by the phenol."); comment("Hold cap tightly so it doesn't open or spill."); //6. add 200 ul TE buffer and spin for 5 min, in microfuge //7. transfer 350 ml aqueous (top) layer to fresh eppendorf. next_step(); measure_and_add(eppendorf1, te, vol(200, UL)); centrifuge_phases(eppendorf1, speed(SPEED_MAX, RPM), RT, time(5, MINS), vol(350, UL), eppendorf2); //8. add 1 ml 95% ethanol and mix well, let sit for 10 minutes next_step(); measure_and_add(eppendorf2, ethanol, vol(1, ML)); vortex(eppendorf2); store_for(eppendorf2, RT, time(10, MINS)); //9. spin for 2 min, take off supernatant, and let dry upside down 10 min. next_step(); centrifuge_pellet(eppendorf2, speed(SPEED_MAX, RPM), RT, time(2, MINS)); invert_dry(eppendorf2, RT, time(10, MINS)); //10. resuspend pellet in 50 ul TE buffer or water. next_step(); begin_option(); measure_and_add(eppendorf2, te, vol(50, UL)); next_option(); measure_and_add(eppendorf2, water, vol(50, UL)); end_option(); resuspend(eppendorf2); comment("You can now use 1-2 ul of this crude yeast plasmid DNA prep to transform E. coli."); end_protocol(); } </code>