Difference between revisions of "Shared Laboratory Notebook"
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See also See http://2014.igem.org/Team:SF_Bay_Area_DIYbio/Notebook | See also See http://2014.igem.org/Team:SF_Bay_Area_DIYbio/Notebook | ||
'''For experiments from January 2016 on, see [[Experiments started January 2016]]''' | |||
'''General Protocols''' | '''General Protocols''' | ||
*[[DNA Handling]] | *[[DNA Handling]] | ||
*[https://www.dna20.com/products/expression-vectors/electra-system#2 Electra cloning protocol] | *[https://www.dna20.com/products/expression-vectors/electra-system#2 Electra cloning protocol] (Used for cloning IDT gBlocks into plasmid backbone) | ||
*[[Media:Zymo E. coli competent cells transformation protocol.pdf]] | *[[Media:Zymo E. coli competent cells transformation protocol.pdf]] (Protocol to transform plasmid DNA into chemically competent ''E. coli'') | ||
*[[Media:D4025i.pdf]] (Zyppy plasmid midiprep protocol) | *[[Media:D4025i.pdf]] (Zyppy plasmid midiprep protocol; used to purify plasmid DNA from ''E. coli'') | ||
*[[Media:Clontech UTF-8'en-us'Quick Easy Yeast Transformation Mix Protocol-At-A-Glance 040214.pdf]] | *[[Media:Clontech UTF-8'en-us'Quick Easy Yeast Transformation Mix Protocol-At-A-Glance 040214.pdf]] (Protocol to transform plasmid DNA into yeast cells) | ||
*[[Sequencing Analysis using Serial Cloner 2-6-1]] | *[[Sequencing Analysis using Serial Cloner 2-6-1]] | ||
*[[Media:5-FOA Protocol, Zymo Research.pdf]] (Using 5-FOA to select against URA3+ yeast strains) | *[[Media:5-FOA Protocol, Zymo Research.pdf]] (Using 5-FOA to select against URA3+ yeast strains) | ||
*[[Media:LifeTech_NuPAGE_TrisGlycine_Mini_Gels_Cat-EC6025BOX.pdf]] (General protocol for precast Tris-Glycine 4%-20% acrylamide protein gels) | |||
'''General Documentation Information''' | '''General Documentation Information''' | ||
| Line 31: | Line 34: | ||
*[[Repeat Midipreps to select new clones for sequencing for failed sequences from Oct. 2]] | *[[Repeat Midipreps to select new clones for sequencing for failed sequences from Oct. 2]] | ||
*[[Cloning human alpha casein S1, 04Oct2014 and on]] | *[[Cloning human alpha casein S1, 04Oct2014 and on]] | ||
*[[Checking for contamination in yeast strains, media, water, and lab surfaces 06Oct2014]] | |||
*[[Cloning bovineKappa and bovineBeta into pSB1C3 Biobrick using NEB biobrick kit 08Oct2014]] | *[[Cloning bovineKappa and bovineBeta into pSB1C3 Biobrick using NEB biobrick kit 08Oct2014]] | ||
*[[Submitting 4 repeat and 1 new casein in pD1214 plasmid for sequencing 10Oct2014]] | *[[Submitting 4 repeat and 1 new casein in pD1214 plasmid for sequencing 10Oct2014]] | ||
| Line 37: | Line 41: | ||
*[[Submitting FAM20C (Kex + & Kex -) for sequencing with new internal primers 14Oct2014]] | *[[Submitting FAM20C (Kex + & Kex -) for sequencing with new internal primers 14Oct2014]] | ||
*[[Submitting FAM20C Kex + clone 9A and bovineKappa and bovineBeta: pSB1C3 Biobrick for sequencing 15Oct2014]] | *[[Submitting FAM20C Kex + clone 9A and bovineKappa and bovineBeta: pSB1C3 Biobrick for sequencing 15Oct2014]] | ||
*[[Electra cloning of #5 Casein insert 22Oct2014]] | |||
*[[Experiment to determine whether yeast is contaminated and to salvage strain using 5FOA, 23Oct2014]] | *[[Experiment to determine whether yeast is contaminated and to salvage strain using 5FOA, 23Oct2014]] | ||
*[[Test yeast transformation Bovine alpha S1 and Bovine beta B caseins 26Oct2014]] | |||
'''November 2014''' | |||
*[[Streaked new colonies of Bovine alpha S1 and Bovine beta B casein yeast transformations 03Nov2014]] | |||
*[[Quantified IDT DNA (human kappa casein kex-) sample on nanodrop spectrophotometer to verify that the resuspension back in September worked.]] 06Nov2014 | |||
*[[Checked for colony growth in 03Nov2014 streak plates. Result: Yes]] 06Nov2014 | |||
*[[Making liquid cultures, in duplicate, of bovine Alpha S1 and bovine Beta B transformed yeast colonies.]] 12Nov2014 | |||
*[[Attempt SDS Page and also mini prep to confirm that yeast transformations worked]] 14Nov2014 | |||
*[[Repeat Mini Prep of bovine alpha S1 and bone beta B yeast]] 17Nov2014 | |||
*[[Yeast Transformation (Clontech kit)]] 18Nov2014 | |||
*[[SDS Page-Gel for all the bovine proteins]] 24Nov2014 | |||
*[[New 5 FOA Plates and prepare media]] 25Nov2014 | |||
'''December 2014''' | |||
*[[Repeat SDS Page-Gel for all the bovine proteins]] 07Dec2014 | |||
'''January 2015''' | |||
*[[Yeast Transformation of All Bovine Casein Inserts]] 10Jan2015 | |||
*[[SDS Page-Gel for all the bovine casein inserts]] 17Jan2015 | |||
'''May 2015''' | |||
*[[Western Blot of bovine casein]] 2May2015 | |||
'''May 2016''' | |||
*[[Plating URA- and Turbo Yeast Control]] 9-10 May 2016 | |||
'''June 2016''' | |||
Latest revision as of 02:49, 15 June 2016
See also See http://2014.igem.org/Team:SF_Bay_Area_DIYbio/Notebook
For experiments from January 2016 on, see Experiments started January 2016
General Protocols
- DNA Handling
- Electra cloning protocol (Used for cloning IDT gBlocks into plasmid backbone)
- Media:Zymo E. coli competent cells transformation protocol.pdf (Protocol to transform plasmid DNA into chemically competent E. coli)
- Media:D4025i.pdf (Zyppy plasmid midiprep protocol; used to purify plasmid DNA from E. coli)
- Media:Clontech UTF-8'en-us'Quick Easy Yeast Transformation Mix Protocol-At-A-Glance 040214.pdf (Protocol to transform plasmid DNA into yeast cells)
- Sequencing Analysis using Serial Cloner 2-6-1
- Media:5-FOA Protocol, Zymo Research.pdf (Using 5-FOA to select against URA3+ yeast strains)
- Media:LifeTech_NuPAGE_TrisGlycine_Mini_Gels_Cat-EC6025BOX.pdf (General protocol for precast Tris-Glycine 4%-20% acrylamide protein gels)
General Documentation Information
June 2014
August 2014
September 2014
- Cloning 7 casein gBlocks, 12Sep2014 and on
- Troubleshooting failed 12Sep2014 transformation of P.FAKS.humBeta.S
- Cloning bovine beta casein, Fam20C (Kex + & -), from 27Sep2014
- Submitting 10 casein and FAM20C in pD1214 plasmids for sequencing 30Sep2014
October 2014
- Initial studies of yeast strains' growth conditions and troubleshooting
- Repeat Midipreps to select new clones for sequencing for failed sequences from Oct. 2
- Cloning human alpha casein S1, 04Oct2014 and on
- Checking for contamination in yeast strains, media, water, and lab surfaces 06Oct2014
- Cloning bovineKappa and bovineBeta into pSB1C3 Biobrick using NEB biobrick kit 08Oct2014
- Submitting 4 repeat and 1 new casein in pD1214 plasmid for sequencing 10Oct2014
- Cloning bovineKappa and bovineBeta into pSB1C3 Biobrick using NEB biobrick kit 10Oct2014
- Cloning bovineBeta into pSB1C3 Biobrick using NEB biobrick kit 13Oct2014
- Submitting FAM20C (Kex + & Kex -) for sequencing with new internal primers 14Oct2014
- Submitting FAM20C Kex + clone 9A and bovineKappa and bovineBeta: pSB1C3 Biobrick for sequencing 15Oct2014
- Electra cloning of #5 Casein insert 22Oct2014
- Experiment to determine whether yeast is contaminated and to salvage strain using 5FOA, 23Oct2014
- Test yeast transformation Bovine alpha S1 and Bovine beta B caseins 26Oct2014
November 2014
- Streaked new colonies of Bovine alpha S1 and Bovine beta B casein yeast transformations 03Nov2014
- Quantified IDT DNA (human kappa casein kex-) sample on nanodrop spectrophotometer to verify that the resuspension back in September worked. 06Nov2014
- Checked for colony growth in 03Nov2014 streak plates. Result: Yes 06Nov2014
- Making liquid cultures, in duplicate, of bovine Alpha S1 and bovine Beta B transformed yeast colonies. 12Nov2014
- Attempt SDS Page and also mini prep to confirm that yeast transformations worked 14Nov2014
- Repeat Mini Prep of bovine alpha S1 and bone beta B yeast 17Nov2014
- Yeast Transformation (Clontech kit) 18Nov2014
- SDS Page-Gel for all the bovine proteins 24Nov2014
- New 5 FOA Plates and prepare media 25Nov2014
December 2014
January 2015
- Yeast Transformation of All Bovine Casein Inserts 10Jan2015
- SDS Page-Gel for all the bovine casein inserts 17Jan2015
May 2015
- Western Blot of bovine casein 2May2015
May 2016
- Plating URA- and Turbo Yeast Control 9-10 May 2016
June 2016