User:Behzad Damadzadeh/Notebook/PcTF Subcloning in E-coli - Revision history

Karmella Haynes at 18:14, 4 April 2012

2012-04-04T18:14:48Z

←Older revision		Revision as of 18:14, 4 April 2012
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	\|-		\|-
	\|colspan="2"\|		\|colspan="2"\|
-	==~~04/04/11~~==	+
-	~~<!-- Precede finished items with a checkmark ✓ -->~~	+	==Behzad's Notebook==
-	* ~~✓ Assemblies: BD111, BD112, BD113~~	+
		+	'''Project Description'''
		+	* Project description coming soon

Karmella Haynes at 18:10, 4 April 2012

2012-04-04T18:10:33Z

←Older revision		Revision as of 18:10, 4 April 2012
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	<!-- Precede finished items with a checkmark ✓ -->		<!-- Precede finished items with a checkmark ✓ -->
	* ✓ Assemblies: BD111, BD112, BD113		* ✓ Assemblies: BD111, BD112, BD113
-	~~----~~
-	~~'''Assemblies'''~~
-	~~# BD111: KAH109/(X/P)/1123 + BBa_B0030/(S/P)/15~~
-	~~# BD112: BD111/(X/P)/1138 + BBa_I712074/(S/P)46~~
-	~~# BD113: BD111/(X/P)/1138 + BBa_I719005/(S/P)23~~
-
-
-	~~> Digests (Fermentas FD)<br>~~
-
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Digest rxn. table -->~~
-	~~\|-valign="top"~~
-	~~\| <u>Reagent</u> \|\| <u>Volume</u> \|\|  ~~
-	~~\| rowspan="9" \|~~
-	\|-
-	~~\| DNA (plasmid) \|\| up to 20 μL~~
-	\|-
-	~~\| 10x buffer \|\| 3.0~~
-	\|-
-	~~\| enzyme 1 \|\| 1.0~~
-	\|-
-	~~\| enzyme 2 \|\| 1.0~~
-	\|-
-	~~\| dH<sub>2</sub>O \|\| ---~~
-	\|-
-	~~\|   \|\| 30 μL --> 37°C/ ~30 min.~~
-	\|}
-	~~{\| class="wikitable" width=400px~~
-	\| Plasmid DNA \|\| 15.0 μl*
-	\|-
-	~~\| Fermentas FastDigest enzyme 1 \|\| 1.0 μl~~
-	\|-
-	~~\| Fermentas FastDigest enzyme 2 \|\| 1.0 μl~~
-	\|-
-	~~\| 10x FastDigest buffer + green loading dye \|\| 3.0 μl~~
-	\|-
-	~~\| dH<sub>2</sub>O \|\| 10.0 μl~~
-	\|-
-	~~\|   \|\| 30.0 μl total~~
-	\|-
-	~~\| colspan="2" \| *For low yield DNA, use up to 25 μL; decrease dH<sub>2</sub>O accordingly.<br>Mix the reaction(s) thoroughly by flicking the tube.<br>Incubate at 37°C for 10 minutes.~~
-	\|}
-	~~__NOTOC__~~

Behzad Damadzadeh at 01:55, 4 April 2012

2012-04-04T01:55:05Z

←Older revision		Revision as of 01:55, 4 April 2012
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	\|   \|\| 30 μL --> 37°C/ ~30 min.		\|   \|\| 30 μL --> 37°C/ ~30 min.
	\|}		\|}
-		+	{\| class="wikitable" width=400px
		+	\| Plasmid DNA \|\| 15.0 μl*
		+	\|-
		+	\| Fermentas FastDigest enzyme 1 \|\| 1.0 μl
		+	\|-
		+	\| Fermentas FastDigest enzyme 2 \|\| 1.0 μl
		+	\|-
		+	\| 10x FastDigest buffer + green loading dye \|\| 3.0 μl
		+	\|-
		+	\| dH<sub>2</sub>O \|\| 10.0 μl
		+	\|-
		+	\|   \|\| 30.0 μl total
		+	\|-
		+	\| colspan="2" \| *For low yield DNA, use up to 25 μL; decrease dH<sub>2</sub>O accordingly.<br>Mix the reaction(s) thoroughly by flicking the tube.<br>Incubate at 37°C for 10 minutes.
		+	\|}
	__NOTOC__		__NOTOC__

Behzad Damadzadeh at 01:50, 4 April 2012

2012-04-04T01:50:00Z

←Older revision		Revision as of 01:50, 4 April 2012
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	\|-valign="top"		\|-valign="top"
	\| <u>Reagent</u> \|\| <u>Volume</u> \|\|		\| <u>Reagent</u> \|\| <u>Volume</u> \|\|
-	\| rowspan="9" \| ~~[[Image:KAH_071211_gel1.tif\|200px\|Cloning digests 7/12/11]]<br>30 μL/lane, 1% agarose -->~~	+	\| rowspan="9" \|
	\|-		\|-
	\| DNA (plasmid) \|\| up to 20 μL		\| DNA (plasmid) \|\| up to 20 μL

Behzad Damadzadeh at 01:47, 4 April 2012

2012-04-04T01:47:44Z

←Older revision		Revision as of 01:47, 4 April 2012
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	==04/04/11==		==04/04/11==
	<!-- Precede finished items with a checkmark ✓ -->		<!-- Precede finished items with a checkmark ✓ -->
-	* ✓ Assemblies: BD111, BD112	+	* ✓ Assemblies: BD111, BD112, BD113
	----		----
	'''Assemblies'''		'''Assemblies'''
-	# ~~KAH213~~: ~~(4) KAH54~~/(S/P)/~~430~~ + ~~(1) KAH210~~/(X/P)/~~2398~~	+	# BD111: KAH109/(X/P)/1123 + BBa_B0030/(S/P)/15
-	# ~~KAH214~~: ~~" + (2) KAH211~~/(X/P)/~~1321~~	+	# BD112: BD111/(X/P)/1138 + BBa_I712074/(S/P)46
-	~~# KAH215: "~~ + ~~(3) KAH212/(X/P)/1621~~	+	# BD113: BD111/(X/P)/1138 + BBa_I719005/(S/P)23
-	~~# KAH216: hPCD~~/(S/P)~~/186 ✓ + KAH210/(X/P)/2398~~	+
-	# ~~KAH217~~: ~~" + KAH211~~/(X/P)/~~1321~~	+
-	~~# KAH218: "~~ + ~~KAH212~~/(X/P)~~/1621~~	+
-	~~# KAH207/V0200: KAH207/(N/S)/1836 ✓ + V0200/(N/S dp)/4442~~	+
-	~~# KAH208/V0200: KAH208/(N/S)/1884 ✓ + "~~	+
-	~~# KAH209/V0200: KAH209/(N/S)/1932 ✓ + "~~	+


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	\| rowspan="9" \| [[Image:KAH_071211_gel1.tif\|200px\|Cloning digests 7/12/11]]<br>30 μL/lane, 1% agarose -->		\| rowspan="9" \| [[Image:KAH_071211_gel1.tif\|200px\|Cloning digests 7/12/11]]<br>30 μL/lane, 1% agarose -->
	\|-		\|-
-	\| DNA (plasmid) \|\| up to 25 μL	+	\| DNA (plasmid) \|\| up to 20 μL
	\|-		\|-
	\| 10x buffer \|\| 3.0		\| 10x buffer \|\| 3.0

Behzad Damadzadeh at 01:06, 4 April 2012

2012-04-04T01:06:42Z

←Older revision		Revision as of 01:06, 4 April 2012
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	\|-		\|-
	\|colspan="2"\|		\|colspan="2"\|
		+	==04/04/11==
		+	<!-- Precede finished items with a checkmark ✓ -->
		+	* ✓ Assemblies: BD111, BD112
	----		----
	'''Assemblies'''		'''Assemblies'''

Behzad Damadzadeh at 01:02, 4 April 2012

2012-04-04T01:02:55Z

←Older revision		Revision as of 01:02, 4 April 2012
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	\|-		\|-
	\|colspan="2"\|		\|colspan="2"\|
-	~~==Project Description~~/~~Abstract==~~	+	----
-	~~[[Image~~:~~engineering_pctfs.jpg\|300px\|thumb\|right\|]]~~	+	'''Assemblies'''
-	* Synthetic biology is an exciting new field that aims to create novel biological functions by artificially combining natural molecular parts. Rational design allows us to engineer the behaviors of protein-based drugs, in ways that we cannot accomplish with small molecule-based drugs. DNA assembly will be used to build a combinatorial library of over 200 synthetic transcription factors (~~Pc-Tfs~~) ~~that will potentially activate therapeutic genes in cancer and stem cells. As time allows, a select group of Pc-TF protein will be purified and analyzed biochemically.~~	+	# KAH213: (4) KAH54/(S/P)/430 + (1) KAH210/(X/P)/2398
		+	# KAH214: " + (2) KAH211/(X/P)/1321
		+	# KAH215: " + (3) KAH212/(X/P)/1621
		+	# KAH216: hPCD/(S/P)/186 ✓ + KAH210/(X/P)/2398
		+	# KAH217: " + KAH211/(X/P)/1321
		+	# KAH218: " + KAH212/(X/P)/1621
		+	# KAH207/V0200: KAH207/(N/S)/1836 ✓ + V0200/(N/S dp)/4442
		+	# KAH208/V0200: KAH208/(N/S)/1884 ✓ + "
		+	# KAH209/V0200: KAH209/(N/S)/1932 ✓ + "

-	~~==Notes==~~
-	* Brady Laughlin's Spring 2012 project in the Haynes Lab at Arizona State University
-	* BME 394 Honors Research Project

		+	> Digests (Fermentas FD)<br>

		+	{\| class="wikitable" border="0" cellspacing="3" <!-- Digest rxn. table -->
		+	\|-valign="top"
		+	\| <u>Reagent</u> \|\| <u>Volume</u> \|\|
		+	\| rowspan="9" \| [[Image:KAH_071211_gel1.tif\|200px\|Cloning digests 7/12/11]]<br>30 μL/lane, 1% agarose -->
	\|-		\|-
-	\|~~colspan="~~2~~" style="background~~-~~color: #F2F2F2;"~~\|	+	\| DNA (plasmid) \|\| up to 25 μL
-	~~{{LnNotebookRecentChanges2}}~~	+	\|-
		+	\| 10x buffer \|\| 3.0
		+	\|-
		+	\| enzyme 1 \|\| 1.0
		+	\|-
		+	\| enzyme 2 \|\| 1.0
		+	\|-
		+	\| dH<sub>2</sub>O \|\| ---
		+	\|-
		+	\|   \|\| 30 μL --> 37°C/ ~30 min.
	\|}		\|}

	__NOTOC__		__NOTOC__

Karmella Haynes at 02:24, 3 April 2012

2012-04-03T02:24:36Z

←Older revision		Revision as of 02:24, 3 April 2012
Line 1:		Line 1:
-		+	{\|{{table}} width="800"
-	~~border~~="1" ~~cellpadding~~="4" ~~cellspacing~~="0" style="~~border~~:#~~c9c9c9 1px solid~~; ~~margin~~: ~~1em 1em 1em 0; border~~-~~collapse~~: ~~collapse~~;"	+	\|-
		+	\|style="background-color: #800000;" align="center"\|
		+	<!-- ## START calendar column -->
		+	<LNCalendar></LNCalendar>
		+	<!-- ## END calendar column -->
		+	\|align="center" style="background-color: #FFCC00;" \|
		+	<!-- ## START search column: Place your logo here. Try keep it below 200px in width and 150px in height. ## -->
		+	[[Image:hayneslab2.jpeg\|128px]] <sitesearch>title=Search this Project</sitesearch>[[Image:atasu.jpeg\|128px]]
		+	<!-- ## END search column ## -->
		+	\|-
		+	\|colspan="2" style="background-color: #F2F2F2;" align="right"\|[[{{FULLPAGENAME}}/Entry_Base\|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page\|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
		+	\|-
		+	\|colspan="2"\|
		+	==Project Description/Abstract==
		+	[[Image:engineering_pctfs.jpg\|300px\|thumb\|right\|]]
		+	* Synthetic biology is an exciting new field that aims to create novel biological functions by artificially combining natural molecular parts. Rational design allows us to engineer the behaviors of protein-based drugs, in ways that we cannot accomplish with small molecule-based drugs. DNA assembly will be used to build a combinatorial library of over 200 synthetic transcription factors (Pc-Tfs) that will potentially activate therapeutic genes in cancer and stem cells. As time allows, a select group of Pc-TF protein will be purified and analyzed biochemically.

	==Notes==		==Notes==
-	* ~~Place some notes here for visitors~~	+	* Brady Laughlin's Spring 2012 project in the Haynes Lab at Arizona State University
-		+	* BME 394 Honors Research Project
-	* ~~Example: This project is currently on hold until further notice.~~	+

Behzad Damadzadeh: User:Behzad Damadzadeh/Notebook/PcTF Subclonning in E-coli moved to User:Behzad Damadzadeh/Notebook/PcTF Subcloning in E-coli

2012-04-03T02:23:20Z

User:Behzad Damadzadeh/Notebook/PcTF Subclonning in E-coli moved to User:Behzad Damadzadeh/Notebook/PcTF Subcloning in E-coli

←Older revision

Revision as of 02:23, 3 April 2012

Behzad Damadzadeh at 01:02, 13 March 2012

2012-03-13T01:02:33Z

←Older revision		Revision as of 01:02, 13 March 2012
Line 1:		Line 1:
-	~~{\|{{table}} width="800"~~
-	\|-
-	~~\|style="background-color: #cdde95;" align="center"\|~~
-	~~<!-- ## START calendar column -->~~
-	~~<LNCalendar></LNCalendar>~~
-	~~<!-- ## END calendar column -->~~
-	~~\|align="center" style="background-color: #e5edc8;" \|~~
-	~~<!-- ## START search column: Place your logo here. Try keep it below 200px in width and 150px in height. ## -->~~
-	~~[[Image:owwnotebook_icon.png\|128px]] <sitesearch>title=Search this Project</sitesearch>~~
-	~~<!-- ## END search column ## -->~~
-	\|-
-	\|colspan="2" style="background-color: #F2F2F2;" align="right"\|[[{{FULLPAGENAME}}/Entry_Base\|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page\|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
-	\|-
-	~~\|colspan="2"\|~~
-
-	~~BioBrick Part Part Number Plate Well Backbone Primer Length~~
-	~~Fw Bw~~
-	~~T7 promoter (strong promoter from T7 bacteriophage) BBa_I712074 2011 Kit Plate 1 6N pSB1AK8 46 bp~~
-	~~T7 Promoter BBa_I719005 2011 Kit Plate 1 15N pSB1A2 VR VF2 23 bp~~
-	~~RBS (Elowitz 1999) -- defines RBS efficiency BBa_B0034 2011 Kit Plate 1 2M pSB1A2 VR VF2 12bp~~
-	~~RBS.1 (strong) -- modified from R. Weiss BBa_B0030 2011 Kit Plate 1 1H pSB1A2 VR VF3 15bp~~
-
-
-
-

		+	border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"

	==Notes==		==Notes==