BME103:T930 Group 13 l2 - Revision history

Ian Bainbirdge: /* Protocols */

Ian Bainbirdge — Thu, 29 Nov 2012 16:58:54 GMT

Protocols

←Older revision		Revision as of 16:58, 29 November 2012
Line 108:		Line 108:
	Stage Three: 72 degrees Celsius for 3 minutes <br>		Stage Three: 72 degrees Celsius for 3 minutes <br>
	Final Hold: 4 degrees Celsius <br>		Final Hold: 4 degrees Celsius <br>
		+	The program is very user friendly and is already pre-programmed so all you need for a basic PCR run is a power source. <br>
		+	The whole process will take about 3 hours to complete due to the amount of time it takes to transition from temperatures. <br>

Marcus J. Sansoni: /* Protocols */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:54:52 GMT

Protocols

←Older revision		Revision as of 16:54, 29 November 2012
Line 58:		Line 58:
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
-	! Supplied in Kit !! Amount	+	\| '''Supplied in Kit''' \|\| '''Amount'''
	\|-		\|-
	\| -PCR machine		\| -PCR machine
	\|-		\|-
-	\| -Buffer \|\| 3200 mL	+	\| -Buffer \|\| -3200 mL
	\|-		\|-
-	\| -Eppendorf \|\| 12	+	\| -Eppendorf \|\| -12
	\|-		\|-
-	\| -Sybr green solution \|\| ~~full~~ Eppendorf tube	+	\| -Sybr green solution \|\| -Full Eppendorf tube
	\|-		\|-
-	\| -DNA calf thymus \|\| 2 microg/mL (full Eppendorf tube)	+	\| -DNA calf thymus \|\| -2 microg/mL (full Eppendorf tube)
	\|-		\|-
-	\| -Pipettes \|\| 20	+	\| -Pipettes \|\| -20
	\|-		\|-
-	\| -Glass slides \|\| 5	+	\| -Glass slides \|\| -5
	\|-		\|-
	\| -Black box		\| -Black box
	\|-		\|-
-	\| -Buffer \|\| 4000mL	+	\| -Buffer \|\| -4000mL
	\|-		\|-
-	\| -Master mix \|\| 100 μL	+	\| -Master mix \|\| -100 μL
	\|-		\|-
	\| -Phone holder		\| -Phone holder

Ian Bainbirdge: /* Protocols */

Ian Bainbirdge — Thu, 29 Nov 2012 16:53:53 GMT

Protocols

←Older revision		Revision as of 16:53, 29 November 2012
Line 101:		Line 101:
	<font size="4">'''PCR Protocol</font>		<font size="4">'''PCR Protocol</font>

-	1. Transfer the PCR reaction mix (50 μL each tube cointaining Taq DNA polymerase, MgCl2, dNTP's, forward primer, reverse prime) into the micro-test tubes which will be used within the PCR machine.	+	1. Transfer the PCR reaction mix (50 μL each tube cointaining Taq DNA polymerase, MgCl2, dNTP's, forward primer, reverse prime) into the micro-test tubes which will be used within the PCR machine. <br>
-	2. Place up to 16 micro test into the PCR Machine and lower and lock the lid.	+	2. Place up to 16 micro test into the PCR Machine and lower and lock the lid. <br>
-	3. Run the open PCR program on a computer connected by usb to the PCR machine and set the cycles to:	+	3. Run the open PCR program on a computer connected by usb to the PCR machine and set the cycles to: <br>
	Stage one: 1 cycle at 95 degrees Celsius for 3 minutes		Stage one: 1 cycle at 95 degrees Celsius for 3 minutes
-	Stage two: 30 cycles at 95 degrees Celsius for 30 seconds, 57 degrees Celsius for 30 seconds, 72 degrees Celsius for 30 seconds	+	Stage two: 30 cycles at 95 degrees Celsius for 30 seconds, 57 degrees Celsius for 30 seconds, 72 degrees Celsius for 30 seconds <br>
-	Stage Three: 72 degrees Celsius for 3 minutes	+	Stage Three: 72 degrees Celsius for 3 minutes <br>
-	Final Hold: 4 degrees Celsius	+	Final Hold: 4 degrees Celsius <br>

Ian Bainbirdge: /* Protocols */

Ian Bainbirdge — Thu, 29 Nov 2012 16:52:53 GMT

Protocols

←Older revision		Revision as of 16:52, 29 November 2012
Line 100:		Line 100:

	<font size="4">'''PCR Protocol</font>		<font size="4">'''PCR Protocol</font>
		+
		+	1. Transfer the PCR reaction mix (50 μL each tube cointaining Taq DNA polymerase, MgCl2, dNTP's, forward primer, reverse prime) into the micro-test tubes which will be used within the PCR machine.
		+	2. Place up to 16 micro test into the PCR Machine and lower and lock the lid.
		+	3. Run the open PCR program on a computer connected by usb to the PCR machine and set the cycles to:
		+	Stage one: 1 cycle at 95 degrees Celsius for 3 minutes
		+	Stage two: 30 cycles at 95 degrees Celsius for 30 seconds, 57 degrees Celsius for 30 seconds, 72 degrees Celsius for 30 seconds
		+	Stage Three: 72 degrees Celsius for 3 minutes
		+	Final Hold: 4 degrees Celsius
		+
		+

Marcus J. Sansoni: /* THE A TEAM */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:50:13 GMT

THE A TEAM

←Older revision		Revision as of 16:50, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~http://openwetware~~.~~org/images/6/6e/Bill.jpg~~\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[Image:Billy.jpg‎\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

Marcus J. Sansoni: /* THE A TEAM */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:48:15 GMT

THE A TEAM

←Older revision		Revision as of 16:48, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[http://openwetware.org/images/6/6e/Bill.jpg~~\|100px~~\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[Image:http://openwetware.org/images/6/6e/Bill.jpg\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

Marcus J. Sansoni: /* THE A TEAM */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:46:09 GMT

THE A TEAM

←Older revision		Revision as of 16:46, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[~~Image:https~~://~~myasucourses~~.~~asu.edu/courses/1/2012Fall-T-BME103-86053-86055-86054/groups~~/~~_185919_1~~//~~_7836695_1~~/~~bill~~.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[http://openwetware.org/images/6/6e/Bill.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

Marcus J. Sansoni: /* THE A TEAM */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:44:20 GMT

THE A TEAM

←Older revision		Revision as of 16:44, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~Windows Photo Gallery Wallpaper~~.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[Image:https://myasucourses.asu.edu/courses/1/2012Fall-T-BME103-86053-86055-86054/groups/_185919_1//_7836695_1/bill.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

Marcus J. Sansoni: /* Thermal Cycler Engineering */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:41:17 GMT

Thermal Cycler Engineering

←Older revision		Revision as of 16:41, 29 November 2012
Line 32:		Line 32:
	'''System Design'''<br> The Heat Sink Fan moves air across the metal sheets to cool down the PCR machine and the samples. The Heat Sink removes heat from the PCR machine to cool down the samples. It does this by conducting heat down to the metal sheets that are located beside the heat sink fan.		'''System Design'''<br> The Heat Sink Fan moves air across the metal sheets to cool down the PCR machine and the samples. The Heat Sink removes heat from the PCR machine to cool down the samples. It does this by conducting heat down to the metal sheets that are located beside the heat sink fan.

-	'''Key Features'''<br> For the Heat Sink Fan, we want to add a second fan to the PCR machine. The reason for adding an additional fan would be cool the heat sink down more rapidly. We also want to change the heat sink in general by add more surface area to the metal sheets in the center. We would increase the number of sheets vertically, reducing space between sheets, and we would also add two to three sheets horizontally, to increase the surface area even more.	+	'''Key Features'''<br> For the Heat Sink Fan, we want to add a second fan to the PCR machine. The reason for adding an additional fan would be cool the heat sink down more rapidly. If we are able to cool the heat sink down faster it would speed up the whole process all together. We also want to change the heat sink in general by add more surface area to the metal sheets in the center. We would increase the number of sheets vertically, reducing space between sheets, and we would also add two to three sheets horizontally, to increase the surface area even more. Adding more surface allows the heat sink to drain heat more rapidly, which then cuts down the transition between cycles.

	'''Instructions'''<br> The instructions for assembly or use of the machine would not change. To add the second fan, though, we would have to expand the exterior walls to make room for it. This would make the machine slightly larger, but not change its compact, portable size.		'''Instructions'''<br> The instructions for assembly or use of the machine would not change. To add the second fan, though, we would have to expand the exterior walls to make room for it. This would make the machine slightly larger, but not change its compact, portable size.

Marcus J. Sansoni: /* Protocols */

Marcus J. Sansoni — Thu, 29 Nov 2012 16:38:23 GMT

Protocols

←Older revision		Revision as of 16:50, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~http://openwetware~~.~~org/images/6/6e/Bill.jpg~~\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[Image:Billy.jpg‎\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

←Older revision		Revision as of 16:48, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[http://openwetware.org/images/6/6e/Bill.jpg~~\|100px~~\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[Image:http://openwetware.org/images/6/6e/Bill.jpg\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

←Older revision		Revision as of 16:46, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[~~Image:https~~://~~myasucourses~~.~~asu.edu/courses/1/2012Fall-T-BME103-86053-86055-86054/groups~~/~~_185919_1~~//~~_7836695_1~~/~~bill~~.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[http://openwetware.org/images/6/6e/Bill.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

←Older revision		Revision as of 16:44, 29 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~Windows Photo Gallery Wallpaper~~.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]	+	\| [[Image:https://myasucourses.asu.edu/courses/1/2012Fall-T-BME103-86053-86055-86054/groups/_185919_1//_7836695_1/bill.jpg\|100px\|thumb\|Name: Marcus Sansoni<br>Open PCR Machine Engineer]]
	\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]		\| [[Image:Pete_Marple.jpg‎\|100px\|thumb\|Name: Pete Marple<br>Open PCR Machine Engineer]]
	\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]		\| [[Image:Michelle_Lipowicz.jpg‎\|100px\|thumb\|Name: Michelle Lipowicz<br>Experimental Protocol Planner]]

←Older revision		Revision as of 16:38, 29 November 2012
Line 105:		Line 105:

	<font size="4">'''DNA Measurement Protocol'''</font> <br>		<font size="4">'''DNA Measurement Protocol'''</font> <br>
-	1. ~~label~~ each pipette bulb, using sharpie, with the sample name it will be used for (ex: "c+" or "1-3" as in patient 1-replicate 3)<br>	+	1. Label each pipette bulb, using sharpie, with the sample name it will be used for (ex: "c+" or "1-3" as in patient 1-replicate 3)<br>
	2. label each Eppendorf tube, using sharpie, with the same name corresponding to the pipette <br>		2. label each Eppendorf tube, using sharpie, with the same name corresponding to the pipette <br>
-	3. ~~using~~ only one designated pipette per sample transfer the each sample into separate Eppendorf tubes filled with 400mL of buffer solution. make sure to label the buffer tube with the corresponding sample name (ex: "c+" or "1-2")<br>	+	3. Using only one designated pipette per sample transfer the each sample into separate Eppendorf tubes filled with 400mL of buffer solution. make sure to label the buffer tube with the corresponding sample name (ex: "c+" or "1-2")<br>
-	4. to set up fluorimeter, slide one glass slide into slit with the gritty side facing up and slide the glass so that the light is aligned between the first two holes<br>	+	4. To set up fluorimeter, slide one glass slide into slit with the gritty side facing up and slide the glass so that the light is aligned between the first two holes<br>
-	5. ~~using~~ pipette designated for sample , place one drop on each of the two holes on the glass slide <br>	+	5. Using pipette designated for sample , place one drop on each of the two holes on the glass slide <br>
-	6. ~~using~~ pipette designated for sybr green solution, place two drops in between the two drops of sample, this should create one big drop of liquid<br>	+	6. Using pipette designated for sybr green solution, place two drops in between the two drops of sample, this should create one big drop of liquid<br>
-	7. ~~realign~~ the light to make sure it is going through the drop of liquid <br>	+	7. Realign the light to make sure it is going through the drop of liquid <br>
-	8. ~~place~~ smart phone is phone holder and set in front of fluorimeter making sure camera can clearly see drop of liquid <br>	+	8. Place smart phone is phone holder and set in front of fluorimeter making sure camera can clearly see drop of liquid <br>
-	9. ~~place~~ black box over phone in holder and flourimeter to darken area <br>	+	9. Place black box over phone in holder and flourimeter to darken area <br>
-	10. ~~press~~ screen camera on the drop to focus camera <br>	+	10. Press screen camera on the drop to focus camera <br>
-	11. ~~take~~ picture of drop covering area from light as best as possible<br>	+	11. Take picture of drop covering area from light as best as possible<br>
-	12. ~~once~~ picture is taken, make sure to write down the name of the picture in the phone as it corresponds to the sample in a chart<br>	+	12. Once picture is taken, make sure to write down the name of the picture in the phone as it corresponds to the sample in a chart<br>
-	13. ~~using~~ a pipette designated for waste, suck up the drop, squeeze into waste cup, and slide glass so that light is between the next two holes<br>	+	13. Using a pipette designated for waste, suck up the drop, squeeze into waste cup, and slide glass so that light is between the next two holes<br>
-	14. ~~repeat~~ steps 5 through 13 for all patients samples and controls, keep in mind that each slide can run five samples so glass slides must be changed every 5 samples<br>	+	14. Repeat steps 5 through 13 for all patients samples and controls, keep in mind that each slide can run five samples so glass slides must be changed every 5 samples<br>
-	15.~~for~~ water sample, place three drops on the glass slide (one on each hole and one in the middle) to create one drop of pure water and follow steps 7 through 13<br>	+	15. For water sample, place three drops on the glass slide (one on each hole and one in the middle) to create one drop of pure water and follow steps 7 through 13<br>
	16. follow step 15 for calf thymus instead of water <br>		16. follow step 15 for calf thymus instead of water <br>
	17. after all pictures are taken, send them to email. make sure that each picture is label with which sample when sending picture to avoid mixups.<br>		17. after all pictures are taken, send them to email. make sure that each picture is label with which sample when sending picture to avoid mixups.<br>