Chromosomal DNA isolation from E. coli protocol - source code

#include "BioCoder.h"

void main()
{
	start_protocol("Chromosomal DNA isolation from E.coli");

	Fluid culture = new_fluid("culture grown in your favorite medium");
	Fluid killing_buffer = new_fluid("Killing Buffer", ICE_COLD);
	Fluid te = new_fluid("TE");
	Fluid sds = new_fluid("10% SDS");
	Fluid edta = new_fluid("0.5M EDTA");
	Fluid isopropanol = new_fluid("isopropanol");
	Fluid rnase = new_fluid("RNase A", "25mg/ml");
	Fluid proteinasek = new_fluid("proteinase K", "25mg/ml");
	Fluid ethanol = new_fluid("ethanol");
	Fluid naac = new_fluid("3M Na-Acetate");
	Fluid water = new_fluid("distilled water");

	Container eppendorf1 = new_container(EPPENDORF, culture);

	//	    *  grow culture in your favorite medium
	//    * Mix samples directly with ice cold Killing Buffer in ratio 1:1 and put on ice (samples should be processed as fast as possible)
	first_step();
	measure_prop(eppendorf1, killing_buffer, 1);
	vortex(eppendorf1);
	store(eppendorf1, ON_ICE);
	comment("Samples should be processed as fast as possible.");

	//    * Spin down cells 3 min max. speed at 4°C and discard supernatant
	next_step();
	centrifuge_pellet(eppendorf1, speed(SPEED_MAX, RPM), 4, time(3, MINS));

	//    * resuspend in 300μL TE and add 40μL 10%SDS and 3μL 0.5M EDTA
	next_step();
	measure_fluid(te, vol(300, UL), eppendorf1);
	measure_fluid(sds, vol(40, UL), eppendorf1);
	measure_fluid(edta, vol(3, UL), eppendorf1);
	resuspend(eppendorf1);

	//    * incubate 5 min at 65°C
	next_step();
	incubate(eppendorf1, 65, time(5, MINS));

	//    * add 750μL isopropanole and mix
	next_step();
	measure_fluid(isopropanol, vol(750, UL), eppendorf1);
	vortex(eppendorf1);

	//    * spin at max. speed for 5 min
	next_step();
	centrifuge_pellet(eppendorf1, speed(SPEED_MAX, RPM), RT, time(5, MINS));

	//    * resuspend pellet in 500μL TE and add 2μL RNase A (25mg/ml)
	next_step();
	measure_fluid(te, vol(500, UL), eppendorf1);
	measure_fluid(rnase, vol(2, UL), eppendorf1);
	resuspend(eppendorf1);

	//    * incubate for 30 min at 65°C
	next_step();
	incubate(eppendorf1, 65, time(30, MINS));

	//    * add 2μL proteinase K (25mg/ml) and incubate at 37°C for 15 min
	next_step();
	measure_fluid(proteinasek, vol(2, UL), eppendorf1);
	incubate(eppendorf1, 37, time(15, MINS));

	//    * phenol extract (2x phenol & 2x chlorophorm)
	next_step();
	to_do("phenol extract (2x phenol & 2x chlorophorm).");

	//    * precipitate over night with 1ml ethanol and 40μL 3M Na-Acetate
	next_step();
	measure_fluid(ethanol, vol(1, ML), eppendorf1);
	measure_fluid(naac, vol(40, UL), eppendorf1);
	store_for(eppendorf1, RT, time(12, HRS));

	//    * spin down DNA at 4°C for 15 min, wash in 70% ethanol and resuspend pellet in 50μL dH2O 
	next_step();
	centrifuge_pellet(eppendorf1, speed(SPEED_MAX, RPM), 4, time(15, MINS));
	measure_fluid(water, vol(50, UL), eppendorf1);
	resuspend(eppendorf1);

	end_protocol();
}