BME103:TEMPwu1 - Revision history

Karmella Haynes at 03:04, 22 March 2013

2013-03-22T03:04:22Z

←Older revision		Revision as of 03:04, 22 March 2013
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	'''The Original Design'''<br>		'''The Original Design'''<br>
-	(Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is)<br>	+	(Add image of the full OpenPCR machine here, from the Week 3 exercise. Write a paragraph description for visitors who have no idea what this is)<br>


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	==Protocols==		==Protocols==

-	'''~~Thermal Cycler Program~~'''<br>	+	'''Polymerase Chain Reaction'''<br>

		+	(Add your work from Week 3, Part 1 here)<br>

-	~~'''DNA Sample Set-up'''<br>~~

-	~~{\| {{table}}~~	+	'''Flourimeter Measurements'''<br>
-	\|-	+
-	~~\| row 1 cell 1 \|\| row 1 cell 2 \|\| row 1 cell 3 \|\| row 1 cell 4~~	+
-	\|-	+
-	~~\| row 2 cell 1 \|\| row 2 cell 2 \|\| row 2 cell 3 \|\| row 2 cell 4~~	+
-	\|}	+

		+	(Add your work from Week 3, Part 2 here)<br>

-	~~'''DNA Sample Set-up Procedure'''~~
-	~~# Step 1~~
-	~~# Step 2~~
-	~~# Step 3...~~

		+	<br><br>
		+	==Research and Development==

-	'''~~PCR Reaction Mix~~'''	+	'''Specific Cancer Marker Detection - The Underlying Technology'''<br>
-	* What is in the PCR reaction mix?	+
-		+
-		+
-	~~'''DNA/ primer mix'''~~	+
-	* What is in the DNA/ primer mix?	+

		+	(Add a write-up of the information discussed in Week 3's class)<br>

		+	(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)


	<br><br>		<br><br>

-	==~~Research and Development~~==	+	==Results==

-	~~'''Specific Cancer Marker Detection - The Underlying Technology'''~~<br>	+	<!--- Place two small Image J data images here. One showing the result of Water and the other showing the result of Calf Thymus DNA --->

-	~~(Add a write-up of the information discussed in Week 3's class)<br>~~

-	~~(BONUS points: Use a program like Powerpoint~~, ~~Word, Illustrator, Microsoft Paint~~, etc. ~~to illustrate how primers bind to~~ the ~~cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures~~ from ~~the OpenPCR tutorial might be useful. Be sure to credit the source if~~ you ~~borrow images~~.)	+	<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->
		+	{\| {{table}}
		+	\|- style="background:#f0f0f0;"
		+	\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''
		+	\|-
		+	\| PCR: Negative Control \|\| E6 \|\| F6 \|\| G6
		+	\|-
		+	\| PCR: Positive Control \|\| E7 \|\| F7 \|\| G7
		+	\|-
		+	\| PCR: Patient 1 ID #####, rep 1 \|\| E8 \|\| F8 \|\| G8
		+	\|-
		+	\| PCR: Patient 1 ID #####, rep 2 \|\| E9 \|\| F9 \|\| G9
		+	\|-
		+	\| PCR: Patient 1 ID #####, rep 3 \|\| E10 \|\| F10 \|\| G10
		+	\|-
		+	\| PCR: Patient 2 ID #####, rep 1 \|\| E11 \|\| F11 \|\| G11
		+	\|-
		+	\| PCR: Patient 2 ID #####, rep 2 \|\| E12 \|\| F12 \|\| G12
		+	\|-
		+	\| PCR: Patient 2 ID #####, rep 3 \|\| E13 \|\| F13 \|\| G13
		+	\|}


-	<br><br>	+	KEY
		+	* '''Sample''' = <!--- explain what "sample" means --->
		+	* '''Integrated Density''' = <!--- explain what "integrated density" means and how you did background subtraction to get this value --->
		+	* '''DNA μg/mL''' = <!--- explain how you calculated this --->
		+	* '''Conclusion''' = <!--- explain what "Positive" and "No signal" means, relative to the control samples --->

Karmella Haynes: /* Protocols */

2013-03-19T18:01:25Z

Protocols

←Older revision		Revision as of 18:01, 19 March 2013
Line 48:		Line 48:

	'''Thermal Cycler Program'''<br>		'''Thermal Cycler Program'''<br>
		+

	'''DNA Sample Set-up'''<br>		'''DNA Sample Set-up'''<br>
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	\| row 2 cell 1 \|\| row 2 cell 2 \|\| row 2 cell 3 \|\| row 2 cell 4		\| row 2 cell 1 \|\| row 2 cell 2 \|\| row 2 cell 3 \|\| row 2 cell 4
	\|}		\|}
		+

	'''DNA Sample Set-up Procedure'''		'''DNA Sample Set-up Procedure'''
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	# Step 2		# Step 2
	# Step 3...		# Step 3...
		+

	'''PCR Reaction Mix'''		'''PCR Reaction Mix'''
	* What is in the PCR reaction mix?		* What is in the PCR reaction mix?
		+

	'''DNA/ primer mix'''		'''DNA/ primer mix'''
	* What is in the DNA/ primer mix?		* What is in the DNA/ primer mix?
-
-

Karmella Haynes: /* Protocols */

2013-03-19T18:01:05Z

Protocols

←Older revision		Revision as of 18:01, 19 March 2013
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	{\| {{table}}		{\| {{table}}
	\|-		\|-
-	\| row 1 cell 1 \|\| row 1 cell 2	+	\| row 1 cell 1 \|\| row 1 cell 2 \|\| row 1 cell 3 \|\| row 1 cell 4
	\|-		\|-
-	\| row 2 cell 1 \|\| row 2 cell 2	+	\| row 2 cell 1 \|\| row 2 cell 2 \|\| row 2 cell 3 \|\| row 2 cell 4
	\|}		\|}

Karmella Haynes: /* Protocols */

2013-03-19T17:45:37Z

Protocols

←Older revision		Revision as of 17:45, 19 March 2013
Line 47:		Line 47:
	==Protocols==		==Protocols==

-	'''~~Polymerase Chain Reaction~~'''<br>	+	'''Thermal Cycler Program'''<br>

		+	'''DNA Sample Set-up'''<br>

		+	{\| {{table}}
		+	\|-
		+	\| row 1 cell 1 \|\| row 1 cell 2
		+	\|-
		+	\| row 2 cell 1 \|\| row 2 cell 2
		+	\|}
		+
		+	'''DNA Sample Set-up Procedure'''
		+	# Step 1
		+	# Step 2
		+	# Step 3...
		+
		+	'''PCR Reaction Mix'''
		+	* What is in the PCR reaction mix?
		+
		+	'''DNA/ primer mix'''
		+	* What is in the DNA/ primer mix?


-	~~'''Flourimeter Measurements'''<br>~~


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	<br><br>		<br><br>
		+
	==Research and Development==		==Research and Development==

Karmella Haynes at 17:19, 19 March 2013

2013-03-19T17:19:33Z

←Older revision		Revision as of 17:19, 19 March 2013
Line 27:		Line 27:

	'''The Original Design'''<br>		'''The Original Design'''<br>
-	(Add image of the full OpenPCR machine here, from the Week 3 exercise. Write a paragraph description for visitors who have no idea what this is)<br>	+	(Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is)<br>


Line 49:		Line 49:
	'''Polymerase Chain Reaction'''<br>		'''Polymerase Chain Reaction'''<br>

-	~~(Add your work from Week 3, Part 1 here)<br>~~	+


	'''Flourimeter Measurements'''<br>		'''Flourimeter Measurements'''<br>

-	~~(Add your work from Week 3, Part 2 here)<br>~~	+


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	<br><br>		<br><br>
-
-	~~==Results==~~
-
-	~~<!--- Place two small Image J data images here. One showing the result of Water and the other showing the result of Calf Thymus DNA --->~~
-
-
-	~~<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->~~
-	~~{\| {{table}}~~
-	~~\|- style="background:#f0f0f0;"~~
-	~~\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''~~
-	\|-
-	~~\| PCR: Negative Control \|\| E6 \|\| F6 \|\| G6~~
-	\|-
-	~~\| PCR: Positive Control \|\| E7 \|\| F7 \|\| G7~~
-	\|-
-	~~\| PCR: Patient 1 ID #####, rep 1 \|\| E8 \|\| F8 \|\| G8~~
-	\|-
-	~~\| PCR: Patient 1 ID #####, rep 2 \|\| E9 \|\| F9 \|\| G9~~
-	\|-
-	~~\| PCR: Patient 1 ID #####, rep 3 \|\| E10 \|\| F10 \|\| G10~~
-	\|-
-	~~\| PCR: Patient 2 ID #####, rep 1 \|\| E11 \|\| F11 \|\| G11~~
-	\|-
-	~~\| PCR: Patient 2 ID #####, rep 2 \|\| E12 \|\| F12 \|\| G12~~
-	\|-
-	~~\| PCR: Patient 2 ID #####, rep 3 \|\| E13 \|\| F13 \|\| G13~~
-	\|}
-
-
-	~~KEY~~
-	* '''Sample''' = <!--- explain what "sample" means --->
-	* '''Integrated Density''' = <!--- explain what "integrated density" means and how you did background subtraction to get this value --->
-	* '''DNA μg/mL''' = <!--- explain how you calculated this --->
-	* '''Conclusion''' = <!--- explain what "Positive" and "No signal" means, relative to the control samples --->

Karmella Haynes: /* Results */

2012-11-09T21:22:46Z

Results

←Older revision		Revision as of 21:22, 9 November 2012
Line 100:		Line 100:
	* '''Sample''' = <!--- explain what "sample" means --->		* '''Sample''' = <!--- explain what "sample" means --->
	* '''Integrated Density''' = <!--- explain what "integrated density" means and how you did background subtraction to get this value --->		* '''Integrated Density''' = <!--- explain what "integrated density" means and how you did background subtraction to get this value --->
-	* '''DNA μg/mL''' = <!--- how you calculated this --->	+	* '''DNA μg/mL''' = <!--- explain how you calculated this --->
-	* '''Conclusion''' = <!--- explain	+	* '''Conclusion''' = <!--- explain what "Positive" and "No signal" means, relative to the control samples --->

Karmella Haynes: /* Results */

2012-11-09T20:53:32Z

Results

←Older revision		Revision as of 20:53, 9 November 2012
Line 71:		Line 71:
	==Results==		==Results==

-	<!--- Place two small images here. One showing Water ~~in Image J~~ and ~~one~~ showing Calf Thymus DNA --->	+	<!--- Place two small Image J data images here. One showing the result of Water and the other showing the result of Calf Thymus DNA --->


	<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->		<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->
-	{\| ~~class="wikitable"~~ style="~~width~~:~~500px~~; ~~cellspacing:2px; cellpadding=2px;"~~	+	{\| {{table}}
-	~~\|- bgcolor="lightgrey~~"	+	\|- style="background:#f0f0f0;"
-	\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''	+	\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''
	\|-		\|-
	\| PCR: Negative Control \|\| E6 \|\| F6 \|\| G6		\| PCR: Negative Control \|\| E6 \|\| F6 \|\| G6

Karmella Haynes: /* Results */

2012-11-09T20:27:47Z

Results

←Older revision		Revision as of 20:27, 9 November 2012
Line 74:		Line 74:


		+	<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->
	{\| class="wikitable" style="width:500px; cellspacing:2px; cellpadding=2px;"		{\| class="wikitable" style="width:500px; cellspacing:2px; cellpadding=2px;"
	\|- bgcolor="lightgrey"		\|- bgcolor="lightgrey"

Karmella Haynes: /* Results */

2012-11-09T08:42:09Z

Results

←Older revision		Revision as of 08:42, 9 November 2012
Line 82:		Line 82:
	\| PCR: Positive Control \|\| E7 \|\| F7 \|\| G7		\| PCR: Positive Control \|\| E7 \|\| F7 \|\| G7
	\|-		\|-
-	\| PCR: ~~Patientn~~ 1 ID #####, rep 1 \|\| E8 \|\| F8 \|\| G8	+	\| PCR: Patient 1 ID #####, rep 1 \|\| E8 \|\| F8 \|\| G8
	\|-		\|-
	\| PCR: Patient 1 ID #####, rep 2 \|\| E9 \|\| F9 \|\| G9		\| PCR: Patient 1 ID #####, rep 2 \|\| E9 \|\| F9 \|\| G9

Karmella Haynes: /* Results */

2012-11-09T08:41:28Z

Results

←Older revision		Revision as of 08:41, 9 November 2012
Line 75:		Line 75:

	{\| class="wikitable" style="width:500px; cellspacing:2px; cellpadding=2px;"		{\| class="wikitable" style="width:500px; cellspacing:2px; cellpadding=2px;"
-	\|- bgcolor="~~grey~~"	+	\|- bgcolor="lightgrey"
	\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''		\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''
	\|-		\|-
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	\| PCR: Positive Control \|\| E7 \|\| F7 \|\| G7		\| PCR: Positive Control \|\| E7 \|\| F7 \|\| G7
	\|-		\|-
-	\| PCR: ~~Patient~~ ID #####, rep 1 \|\| E8 \|\| F8 \|\| G8	+	\| PCR: Patientn 1 ID #####, rep 1 \|\| E8 \|\| F8 \|\| G8
	\|-		\|-
-	\| PCR: Patient ID #####, rep 2 \|\| E9 \|\| F9 \|\| G9	+	\| PCR: Patient 1 ID #####, rep 2 \|\| E9 \|\| F9 \|\| G9
		+	\|-
		+	\| PCR: Patient 1 ID #####, rep 3 \|\| E10 \|\| F10 \|\| G10
		+	\|-
		+	\| PCR: Patient 2 ID #####, rep 1 \|\| E11 \|\| F11 \|\| G11
		+	\|-
		+	\| PCR: Patient 2 ID #####, rep 2 \|\| E12 \|\| F12 \|\| G12
		+	\|-
		+	\| PCR: Patient 2 ID #####, rep 3 \|\| E13 \|\| F13 \|\| G13
	\|}		\|}
		+

	KEY		KEY