Haynes Lab:Notebook/ASU iGEM - Revision history

Ryan Muller at 07:13, 17 August 2012

2012-08-17T07:13:43Z

←Older revision		Revision as of 07:13, 17 August 2012
Line 32:		Line 32:
	* Melinda Jenner: Buffers, media (and quality control), preparation of BioBrick registry submissions		* Melinda Jenner: Buffers, media (and quality control), preparation of BioBrick registry submissions
	* Amanda Ispas: Buffers, media (and quality control), preparation of BioBrick registry submissions		* Amanda Ispas: Buffers, media (and quality control), preparation of BioBrick registry submissions
-


Line 66:		Line 65:
	* [https://cfo.asu.edu/ehs Environmental Health & Safety at ASU]		* [https://cfo.asu.edu/ehs Environmental Health & Safety at ASU]
	* [http://ehsaweb.asu.edu/ Individual Training Record]: To check your ASU individual safety training record, log in at the EHS Assistant page. Click the "Individual Training Record" link and then enter your ASU ID.		* [http://ehsaweb.asu.edu/ Individual Training Record]: To check your ASU individual safety training record, log in at the EHS Assistant page. Click the "Individual Training Record" link and then enter your ASU ID.
-
-	~~==Daily Lab Notebook==~~
-
-	~~===6-7-12===~~
-	* Transformation (LSE)
-	~~:* Transformed DNA:~~
-	~~::* lacZ (well 4:12G, I732019)~~
-	~~::* p + lacO (well 1:6G, R0011)~~
-	~~:* Cells: neb10beta (donated)~~
-	~~:* Protocol from: http://www.neb.com/nebecomm/products/productc3019.asp~~
-	~~:* Controls: puc19, no DNA (8 plates)~~
-
-	~~===6-8-12===~~
-	* Transformation results:
-	~~:* puc19: growth~~
-	~~:* negative control: no growth~~
-	~~:* lacZ, lacO: possible small colonies~~
-	* liquid culture in amp media (100 ug / ml):
-	~~:* no growth of lacZ, lacO~~
-	~~:* growth of puc19~~
-
-	~~===6-12-12===~~
-	*DH5a Competent Cell Prep
-	~~:*Streak plated cells on LB no amp plate, let grow overnight~~
-
-	~~===6-13-12===~~
-	* Transformation (LSE)
-	~~:* Transformed DNA:~~
-	~~::* lacZ (well 4:12G, I732019)~~
-	~~::* p + lacO (well 1:6G, R0011)~~
-	~~:* Cells: DH5 alpha (donated)~~
-	~~:* Protocol from: http://openwetware.org/wiki/Haynes:Assembly101 (30 minute transformation)~~
-	~~:* Controls: puc19, no DNA (8 plates)~~
-	* Transformation (istb4, Abhi)
-	~~:* Transformed DNA:~~
-	~~:* Cells:~~
-	~~:* Protocol from:~~
-	~~:* Controls:~~
-	*DH5a Chemically Competent cell prep
-	~~:*Grew 2 seed colonies from streak plate in LB no amp~~
-	~~:*Grew controls to test for contamination~~
-	~~::*Both Seed colonies grew, no contamination present~~
-
-	~~===6-14-12===~~
-	*Competent cell prep
-	~~:*Prepared CaCl<sub>2</sub> buffer solution and CaCl<sub>2</sub> glycerol buffer solution~~
-	~~:*Grew seed colony in 400mL LB no amp~~
-
-	~~===6-15-12===~~
-	*Competent cell prep
-	~~:*Centrifuged falcon test tubes containing liquid colonies~~
-	~~:*Resuspended in CaCl<sub>2</sub> buffer solution and incubated for 15 mins~~
-	~~:*Centrifuged and resuspended in CaCl<sub>2</sub> glycerol buffer solution~~
-	~~:*Chilled overnight~~
-
-	~~===6-16-12===~~
-	*Competent cell prep
-	~~:*Aliquotted 200uL into test tubes~~
-	~~:*Stored in -80C~~
-
-	~~===6-17-12===~~
-	~~:*Streak plated prepared competent cells on LB no amp plate~~
-	~~::*Colonies observed~~
-
-	~~===6-19-12===~~
-	*Transformation (LSE)
-	~~:*Transformed DNA:~~
-	~~::*T7 promoter BBa_I712074~~
-	~~::*Constitutive promoter BBa_J23102~~
-	~~:* Cells: DH5 alpha (donated)~~
-	~~:* Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)~~
-	~~:* Controls: puc19, no DNA~~
-	~~:* Plated 2 copies of each (100 ul, 250 ul) on LB amp plates.~~
-	* Made 50 LB Amp plates.
-
-	~~===6-20-12===~~
-	* Plated negative control on LB Amp plate
-	* Liquid cultures of T7 promoter and constitutive promoter
-	*Transformation (LSE)
-	~~:*Transformed DNA:~~
-	~~::*RBS (well 1:1H BBa_B0030)~~
-	~~::*TetR GFP (well 2:8A Part:BBa_I13522)~~
-	~~:* Cells: DH5 alpha (donated)~~
-	~~:* Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)~~
-	~~:* Controls: puc19, no DNA~~
-
-	~~===6-21-12===~~
-	*Made Liquid Cultures of E.coli transformed with RBS B0030
-	*Made Liquid Cultures of E.coli transformed with TetR GFP
-	*miniprepped and nanodropped T7 promoter BBa_I712074 and Constitutive promoter BBa_J23102 liquid cultures
-	* liquid cultures:
-	~~:* RBS1~~
-	~~:* RBS2 (duplicate_~~
-	~~:* GFP1~~
-	~~:* puc19~~
-	~~:* negative controls~~
-	~~:* 5 ml LB amp~~
-	~~:* overnight cultures~~
-	* replated GFP1 & 2 (duplicates)
-	*Nanodropped plasmid DNA samples
-	~~:*Constitutive promoter 1: __ng/uL~~
-	~~:*Constitutive promoter 2: __ng/uL~~
-	~~:*T7 promoter 1: __ng/uL~~
-	~~:*T7 promoter 2: __ng/uL~~
-
-	~~===6-22-12===~~
-	~~:*Miniprepped liquid cultures: RBS (well 1:1H BBa_B0030) and TetR GFP (well 2:8A Part:BBa_I13522)~~
-
-	~~===6-26-12===~~
-	* Transformation:
-	~~:* Transformed DNA:~~
-	~~::* double terminator (B0017, 2:6K)~~
-	~~::* T7 RNA polymerase (I715038, 2:15C)~~
-	~~::* puc19, negative control~~
-	~~:* Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)~~
-	~~:* Cells: dh5a~~
-
-	~~===6-27-12===~~
-	* 6-26 transformation results:
-	~~:* Controls correct~~
-	~~:* 2x terminator: ~19 colonies~~
-	~~:* RNA pol: 1 colony~~
-	* Liquid cultures including controls
-
-	~~===6-28-12===~~
-	*Miniprepped double terminator (B0017, 2:6K) and T7 RNA polymerase (I715038, 2:15C) liquid cultures
-
-	~~===7-2-12===~~
-	*Cleaned up liquid waste
-	*Made SOB media
-	*Finalized oligos for magainin construct
-
-	~~===7-3-12===~~
-	*Autoclaved SOB media
-	*Added glucose to make SOC media
-	*Nanodropped double terminator (B0017, 2:6K) [DT1: 24.5, DT2: 29.6] and T7 RNA polymerase (I715038, 2:15C) [P1: 64.6, P2: 55.3] liquid cultures
-
-
-	~~===7-4-12===~~
-
-	~~===7-5-12===~~
-	~~===7-6-12===~~
-	~~===7-7-12===~~
-	~~===7-8-12===~~
-	~~===7-9-12===~~
-	~~===7-10-12===~~
-	~~===7-11-12===~~
-	~~===7-12-12===~~
-	~~===7-13-12===~~
-	~~===7-14-12===~~
-	~~===7-15-12===~~
-	~~===7-16-12===~~
-	~~===7-17-12===~~
-	~~===7-18-12===~~
-	~~===7-19-12===~~
-	~~===7-20-12===~~
-


	__NOTOC__		__NOTOC__

Ryan Muller: /* Daily Lab Notebook */

2012-08-12T22:44:37Z

Daily Lab Notebook

←Older revision		Revision as of 22:44, 12 August 2012
Line 202:		Line 202:
	*Added glucose to make SOC media		*Added glucose to make SOC media
	*Nanodropped double terminator (B0017, 2:6K) [DT1: 24.5, DT2: 29.6] and T7 RNA polymerase (I715038, 2:15C) [P1: 64.6, P2: 55.3] liquid cultures		*Nanodropped double terminator (B0017, 2:6K) [DT1: 24.5, DT2: 29.6] and T7 RNA polymerase (I715038, 2:15C) [P1: 64.6, P2: 55.3] liquid cultures
-	\|-	+
-	~~\|colspan="2" style="background-color: #F2F2F2;"\|~~	+
-	\|}	+

	===7-4-12===		===7-4-12===
		+
	===7-5-12===		===7-5-12===
	===7-6-12===		===7-6-12===

Ryan Muller: /* 7-3-12 */

2012-08-12T22:41:47Z

7-3-12

←Older revision		Revision as of 22:41, 12 August 2012
Line 205:		Line 205:
	\|colspan="2" style="background-color: #F2F2F2;"\|		\|colspan="2" style="background-color: #F2F2F2;"\|
	\|}		\|}
		+
		+	===7-4-12===
		+	===7-5-12===
		+	===7-6-12===
		+	===7-7-12===
		+	===7-8-12===
		+	===7-9-12===
		+	===7-10-12===
		+	===7-11-12===
		+	===7-12-12===
		+	===7-13-12===
		+	===7-14-12===
		+	===7-15-12===
		+	===7-16-12===
		+	===7-17-12===
		+	===7-18-12===
		+	===7-19-12===
		+	===7-20-12===
		+


	__NOTOC__		__NOTOC__

Ryan Muller: /* Daily Lab Notebook */

2012-08-12T22:39:34Z

Daily Lab Notebook

←Older revision		Revision as of 22:39, 12 August 2012
Line 68:		Line 68:

	==Daily Lab Notebook==		==Daily Lab Notebook==
		+
		+	===6-7-12===
		+	* Transformation (LSE)
		+	:* Transformed DNA:
		+	::* lacZ (well 4:12G, I732019)
		+	::* p + lacO (well 1:6G, R0011)
		+	:* Cells: neb10beta (donated)
		+	:* Protocol from: http://www.neb.com/nebecomm/products/productc3019.asp
		+	:* Controls: puc19, no DNA (8 plates)
		+
		+	===6-8-12===
		+	* Transformation results:
		+	:* puc19: growth
		+	:* negative control: no growth
		+	:* lacZ, lacO: possible small colonies
		+	* liquid culture in amp media (100 ug / ml):
		+	:* no growth of lacZ, lacO
		+	:* growth of puc19
		+
		+	===6-12-12===
		+	*DH5a Competent Cell Prep
		+	:*Streak plated cells on LB no amp plate, let grow overnight
		+
		+	===6-13-12===
		+	* Transformation (LSE)
		+	:* Transformed DNA:
		+	::* lacZ (well 4:12G, I732019)
		+	::* p + lacO (well 1:6G, R0011)
		+	:* Cells: DH5 alpha (donated)
		+	:* Protocol from: http://openwetware.org/wiki/Haynes:Assembly101 (30 minute transformation)
		+	:* Controls: puc19, no DNA (8 plates)
		+	* Transformation (istb4, Abhi)
		+	:* Transformed DNA:
		+	:* Cells:
		+	:* Protocol from:
		+	:* Controls:
		+	*DH5a Chemically Competent cell prep
		+	:*Grew 2 seed colonies from streak plate in LB no amp
		+	:*Grew controls to test for contamination
		+	::*Both Seed colonies grew, no contamination present
		+
		+	===6-14-12===
		+	*Competent cell prep
		+	:*Prepared CaCl<sub>2</sub> buffer solution and CaCl<sub>2</sub> glycerol buffer solution
		+	:*Grew seed colony in 400mL LB no amp
		+
		+	===6-15-12===
		+	*Competent cell prep
		+	:*Centrifuged falcon test tubes containing liquid colonies
		+	:*Resuspended in CaCl<sub>2</sub> buffer solution and incubated for 15 mins
		+	:*Centrifuged and resuspended in CaCl<sub>2</sub> glycerol buffer solution
		+	:*Chilled overnight
		+
		+	===6-16-12===
		+	*Competent cell prep
		+	:*Aliquotted 200uL into test tubes
		+	:*Stored in -80C
		+
		+	===6-17-12===
		+	:*Streak plated prepared competent cells on LB no amp plate
		+	::*Colonies observed
		+
		+	===6-19-12===
		+	*Transformation (LSE)
		+	:*Transformed DNA:
		+	::*T7 promoter BBa_I712074
		+	::*Constitutive promoter BBa_J23102
		+	:* Cells: DH5 alpha (donated)
		+	:* Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)
		+	:* Controls: puc19, no DNA
		+	:* Plated 2 copies of each (100 ul, 250 ul) on LB amp plates.
		+	* Made 50 LB Amp plates.
		+
		+	===6-20-12===
		+	* Plated negative control on LB Amp plate
		+	* Liquid cultures of T7 promoter and constitutive promoter
		+	*Transformation (LSE)
		+	:*Transformed DNA:
		+	::*RBS (well 1:1H BBa_B0030)
		+	::*TetR GFP (well 2:8A Part:BBa_I13522)
		+	:* Cells: DH5 alpha (donated)
		+	:* Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)
		+	:* Controls: puc19, no DNA
		+
		+	===6-21-12===
		+	*Made Liquid Cultures of E.coli transformed with RBS B0030
		+	*Made Liquid Cultures of E.coli transformed with TetR GFP
		+	*miniprepped and nanodropped T7 promoter BBa_I712074 and Constitutive promoter BBa_J23102 liquid cultures
		+	* liquid cultures:
		+	:* RBS1
		+	:* RBS2 (duplicate_
		+	:* GFP1
		+	:* puc19
		+	:* negative controls
		+	:* 5 ml LB amp
		+	:* overnight cultures
		+	* replated GFP1 & 2 (duplicates)
		+	*Nanodropped plasmid DNA samples
		+	:*Constitutive promoter 1: __ng/uL
		+	:*Constitutive promoter 2: __ng/uL
		+	:*T7 promoter 1: __ng/uL
		+	:*T7 promoter 2: __ng/uL
		+
		+	===6-22-12===
		+	:*Miniprepped liquid cultures: RBS (well 1:1H BBa_B0030) and TetR GFP (well 2:8A Part:BBa_I13522)
		+
		+	===6-26-12===
		+	* Transformation:
		+	:* Transformed DNA:
		+	::* double terminator (B0017, 2:6K)
		+	::* T7 RNA polymerase (I715038, 2:15C)
		+	::* puc19, negative control
		+	:* Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)
		+	:* Cells: dh5a
		+
		+	===6-27-12===
		+	* 6-26 transformation results:
		+	:* Controls correct
		+	:* 2x terminator: ~19 colonies
		+	:* RNA pol: 1 colony
		+	* Liquid cultures including controls
		+
		+	===6-28-12===
		+	*Miniprepped double terminator (B0017, 2:6K) and T7 RNA polymerase (I715038, 2:15C) liquid cultures
		+
		+	===7-2-12===
		+	*Cleaned up liquid waste
		+	*Made SOB media
		+	*Finalized oligos for magainin construct
		+
		+	===7-3-12===
		+	*Autoclaved SOB media
		+	*Added glucose to make SOC media
		+	*Nanodropped double terminator (B0017, 2:6K) [DT1: 24.5, DT2: 29.6] and T7 RNA polymerase (I715038, 2:15C) [P1: 64.6, P2: 55.3] liquid cultures
		+	\|-
		+	\|colspan="2" style="background-color: #F2F2F2;"\|
		+	\|}
		+

	__NOTOC__		__NOTOC__

Ryan Muller: /* Daily Lab Notebook */

2012-08-12T22:37:42Z

Daily Lab Notebook

←Older revision		Revision as of 22:37, 12 August 2012
Line 33:		Line 33:
	* Amanda Ispas: Buffers, media (and quality control), preparation of BioBrick registry submissions		* Amanda Ispas: Buffers, media (and quality control), preparation of BioBrick registry submissions

-	~~==Daily Lab Notebook==~~	+

	==BioBricks==		==BioBricks==

Ryan Muller at 22:37, 12 August 2012

2012-08-12T22:37:21Z

Show changes

Ryan Muller: /* Daily Lab Notebook */

2012-08-12T22:35:03Z

Daily Lab Notebook

Show changes

Ryan Muller: /* Project Description/Abstract */

2012-08-12T22:34:45Z

Project Description/Abstract

←Older revision		Revision as of 22:34, 12 August 2012
Line 33:		Line 33:
	* Amanda Ispas: Buffers, media (and quality control), preparation of BioBrick registry submissions		* Amanda Ispas: Buffers, media (and quality control), preparation of BioBrick registry submissions

		+	==Daily Lab Notebook==

	==BioBricks==		==BioBricks==

Karmella Haynes at 01:27, 26 July 2012

2012-07-26T01:27:47Z

←Older revision		Revision as of 01:27, 26 July 2012
Line 58:		Line 58:
	* [http://www.rcsb.org/pdb/home/home.do Protein Data Bank (PDB)]: search for, view, and download full atomic coordinate data for 3D structures of proteins and other molecules. Get tips on editing Jmol 3D images at the [http://openwetware.org/wiki/Haynes:Jmol_Guide Haynes Lab OWW site].		* [http://www.rcsb.org/pdb/home/home.do Protein Data Bank (PDB)]: search for, view, and download full atomic coordinate data for 3D structures of proteins and other molecules. Get tips on editing Jmol 3D images at the [http://openwetware.org/wiki/Haynes:Jmol_Guide Haynes Lab OWW site].
	* [http://openwetware.org/wiki/Haynes:Protocols Protocols - Haynes Lab]: some protocols from the Haynes Lab		* [http://openwetware.org/wiki/Haynes:Protocols Protocols - Haynes Lab]: some protocols from the Haynes Lab
		+
		+	==General Lab Links==
		+	* [https://docs.google.com/spreadsheet/ccc?key=0AghpgNgJLx-ldGtGSUhRRjFRQ0VCdlo4WXdyNlVwWVE Ordering Spreadsheet]

	==Safety==		==Safety==

Karmella Haynes at 18:49, 18 July 2012

2012-07-18T18:49:59Z

←Older revision		Revision as of 18:49, 18 July 2012
Line 53:		Line 53:


-	==Resources==	+	==Science Resources==
	* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ A Plasmid Editor (ApE)]: freeware for viewing, editing, annotating, translating, and finding restriction sites in DNA sequences		* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ A Plasmid Editor (ApE)]: freeware for viewing, editing, annotating, translating, and finding restriction sites in DNA sequences
	* [http://gcat.davidson.edu/igem10/ Oligator]: tool for creating BioBricks using oligo assembly		* [http://gcat.davidson.edu/igem10/ Oligator]: tool for creating BioBricks using oligo assembly
	* [http://www.rcsb.org/pdb/home/home.do Protein Data Bank (PDB)]: search for, view, and download full atomic coordinate data for 3D structures of proteins and other molecules. Get tips on editing Jmol 3D images at the [http://openwetware.org/wiki/Haynes:Jmol_Guide Haynes Lab OWW site].		* [http://www.rcsb.org/pdb/home/home.do Protein Data Bank (PDB)]: search for, view, and download full atomic coordinate data for 3D structures of proteins and other molecules. Get tips on editing Jmol 3D images at the [http://openwetware.org/wiki/Haynes:Jmol_Guide Haynes Lab OWW site].
	* [http://openwetware.org/wiki/Haynes:Protocols Protocols - Haynes Lab]: some protocols from the Haynes Lab		* [http://openwetware.org/wiki/Haynes:Protocols Protocols - Haynes Lab]: some protocols from the Haynes Lab
		+
		+	==Safety==
		+	* [https://cfo.asu.edu/ehs Environmental Health & Safety at ASU]
		+	* [http://ehsaweb.asu.edu/ Individual Training Record]: To check your ASU individual safety training record, log in at the EHS Assistant page. Click the "Individual Training Record" link and then enter your ASU ID.


	__NOTOC__		__NOTOC__