McClean:Protocols: Difference between revisions
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==Basics== | ==Basics== | ||
*[[McClean: Lab Expectations | Lab Expectations]] | |||
*[[McClean: Lab Rules | Lab Rules]] | *[[McClean: Lab Rules | Lab Rules]] | ||
*[[McClean: Lab Jobs| Lab Jobs]] | |||
*[[McClean: Joining The Lab |Joining the Lab]] | *[[McClean: Joining The Lab |Joining the Lab]] | ||
*[[McClean: Leaving The Lab | Leaving the Lab]] | *[[McClean: Leaving The Lab | Leaving the Lab]] | ||
| Line 8: | Line 10: | ||
*[[McClean: Dilution_of_Oligos | Dilution of Oligos]] | *[[McClean: Dilution_of_Oligos | Dilution of Oligos]] | ||
*[[McClean: Ordering_Media | Ordering Media]] | *[[McClean: Ordering_Media | Ordering Media]] | ||
*[[McClean: Order Supplies | Ordering Supplies]] | |||
*[[McClean: Protocol Template| Protocol Template]] | *[[McClean: Protocol Template| Protocol Template]] | ||
*[[McClean: Lab Database | Lab Database]] | *[[McClean: Lab Database | Lab Database]] | ||
*[[McClean: Lab Organization Notes | Lab Organization Notes]] | |||
==Introductory Exercises== | ==Introductory Exercises== | ||
| Line 16: | Line 20: | ||
==Health and Safety== | ==Health and Safety== | ||
*[[McClean: Safety101 | Safety 101]] | *[[McClean: Safety101 | Safety 101]] | ||
*[[McClean: OkToTrash | Ok to Trash Stickers]] | |||
==General Lab Procedures== | ==General Lab Procedures== | ||
| Line 22: | Line 27: | ||
*[[McClean: Pouring Gels for Electrophoresis | Pouring Gels for Electrophoresis (Mike)]] | *[[McClean: Pouring Gels for Electrophoresis | Pouring Gels for Electrophoresis (Mike)]] | ||
*[[McClean: Nanodrop2000 | Using the Nanodrop2000]] | *[[McClean: Nanodrop2000 | Using the Nanodrop2000]] | ||
*[[McClean:Qubit | Quantifying DNA with the Qubit Fluorometer]] | |||
*[[McClean: OrderingLiquidN2 | Ordering Liquid N2 for Common Lab]] | |||
==Yeast== | ==Yeast== | ||
| Line 28: | Line 35: | ||
*[[McClean:Bayanus Transformation | Bayanus Transformation]] | *[[McClean:Bayanus Transformation | Bayanus Transformation]] | ||
*[[McClean: Cleaning Floating Pin Replicators | Cleaning Floating Pin Replicators]] | *[[McClean: Cleaning Floating Pin Replicators | Cleaning Floating Pin Replicators]] | ||
*[[McClean:FISH | Fluorescence in situ Hybridization (Colin)]] | *[[McClean:FISH | Fluorescence in situ Hybridization (Colin)]] | ||
*[[McClean: FISH (Ping) | Fluorescent in situ Hybridization (Ping)]] | *[[McClean: FISH (Ping) | Fluorescent in situ Hybridization (Ping)]] | ||
*[[McClean: FISH (Gasch) | Fluorescent in situ Hybridization (Gasch Lab Collaboration)]] | |||
*[[McClean: Fixation of Yeast (Bisaria Protocol) | Fixation of Yeast (Bisaria Protocol)]] | *[[McClean: Fixation of Yeast (Bisaria Protocol) | Fixation of Yeast (Bisaria Protocol)]] | ||
*[[McClean: Fixation of Yeast (McClean Protocol) | Fixation of Yeast (McClean Protocol)]] | |||
*[[McClean: Fixation of Yeast (P. Xu Protocol) | Fixation of Yeast (P. Xu Protocol)]] | *[[McClean: Fixation of Yeast (P. Xu Protocol) | Fixation of Yeast (P. Xu Protocol)]] | ||
*[[McClean: Frogging a Serial Dilution| Frogging a Serial Dilution]] | *[[McClean: Frogging a Serial Dilution| Frogging a Serial Dilution]] | ||
| Line 45: | Line 53: | ||
*[[McClean: Plasmid Loss Assay| Plasmid Loss Assay]] | *[[McClean: Plasmid Loss Assay| Plasmid Loss Assay]] | ||
*[[McClean:Random_Spore_Prep |Random Spore Prep]] | *[[McClean:Random_Spore_Prep |Random Spore Prep]] | ||
*[[McClean: Sequencing Colony PCR Product | Sequencing | *[[McClean: Sequencing Colony PCR Product | Sanger Sequencing]] | ||
*[[McClean:Smartstat Startup | Smartstat Startup]] | *[[McClean:Smartstat Startup | Smartstat Startup]] | ||
*[[McClean: Sporulation | Sporulation]] | *[[McClean: Sporulation | Sporulation]] | ||
*[[McClean: Tetrad Dissection | Tetrad Dissection]] | *[[McClean: Tetrad Dissection | Tetrad Dissection]] | ||
*[[McClean:URA Pop-out | URA Pop-out]] | *[[McClean:URA Pop-out | URA Pop-out]] | ||
*[[McClean: Yeast Dubious ORFs | Yeast Dubious ORFs]] | |||
*[[McClean: Yeast Mating Halo Assay | Yeast Mating Halo Assay]] | *[[McClean: Yeast Mating Halo Assay | Yeast Mating Halo Assay]] | ||
*[[McClean: Yeast Nomenclature | Yeast Nomenclature]] | *[[McClean: Yeast Nomenclature | Yeast Nomenclature]] | ||
| Line 71: | Line 80: | ||
==PCR== | ==PCR== | ||
*[[McClean: designing primers | Designing Primers (Yeast)]] | |||
*[[McClean: Colony PCR (Yeast) | Colony PCR (Yeast)]] | |||
*[[McClean:dNTPs | dNTP Stocks]] | *[[McClean:dNTPs | dNTP Stocks]] | ||
*[[McClean:Touchdown_PCR | Touchdown PCR]] | *[[McClean:Touchdown_PCR | Touchdown PCR]] | ||
*[[McClean: Takara PrimeStar PCR | Takara PrimeStar PCR]] | *[[McClean: Takara PrimeStar PCR | Takara PrimeStar PCR]] | ||
*[[McClean: Anneal and Extend | Anneal and Extend]] | *[[McClean: Anneal and Extend | Anneal and Extend]] | ||
*[[McClean: Designing "Yeast Toolkit" compatible primers | Designing "Yeast Toolkit" compatible primers]] | |||
==Other DNA Manipulations== | |||
*[[McClean: Golden Gate-Making a new part | Golden Gate-Making a new part]] | |||
*[[McClean: Golden Gate- Making a multi-part plasmid | Golden Gate-Making a multi-part plasmid]] | |||
==Flow Cytometry== | ==Flow Cytometry== | ||
| Line 85: | Line 101: | ||
==Media== | ==Media== | ||
*[[McClean:KS Amino Acid Supplement | KS Amino Acid Supplement]] | *[[McClean:KS Amino Acid Supplement | KS Amino Acid Supplement]] | ||
*[[McClean:LB1 | LB1]] | |||
*[[McClean:LB2 | LB2]] | |||
*[[McClean:LFM_Recipe | Low Fluorescence Media]] | *[[McClean:LFM_Recipe | Low Fluorescence Media]] | ||
*[[McClean:LFA_Membranes | Low Fluorescence Agar Membranes]] | *[[McClean:LFA_Membranes | Low Fluorescence Agar Membranes]] | ||
| Line 92: | Line 110: | ||
*[[McClean:SC_MediawDrugs | Synthetic Complete (SC) Media w/Drugs]] | *[[McClean:SC_MediawDrugs | Synthetic Complete (SC) Media w/Drugs]] | ||
*[[McClean:SC_Canavanine | Synthetic Complete (SC) Media w/Canavanine]] | *[[McClean:SC_Canavanine | Synthetic Complete (SC) Media w/Canavanine]] | ||
*[[McClean:YNB1 | YNB1 | *[[McClean:YNB1 | YNB1]] | ||
*[[McClean:YNB2 | YNB2]] | |||
*[[McClean:YNB3 | YNB3]] | *[[McClean:YNB3 | YNB3]] | ||
*[[McClean: | *[[McClean:YNB4 | YNB4]] | ||
*[[McClean:YPD2 | YPD2]] | |||
*[[McClean:YPD4 | YPD4]] | |||
*[[McClean:Chloramphenicol media | Chloramphenicol media]] | |||
*[[McClean:Kanamycin media | Kanamycin media]] | |||
*[[McClean:5FOA | 5FOA]] | |||
==Stock Solutions== | ==Stock Solutions== | ||
| Line 106: | Line 130: | ||
*[[McClean: EDTA (0.5M) | EDTA (0.5M)]] | *[[McClean: EDTA (0.5M) | EDTA (0.5M)]] | ||
*[[McClean: Geneticin/G418 Stock Solution | Geneticin/G418 Stock Solution]] | *[[McClean: Geneticin/G418 Stock Solution | Geneticin/G418 Stock Solution]] | ||
*[[McClean: Glucose Solution | Glucose Solution for Media]] | |||
*[[McClean: PBS/0.1%Tween| PBS/0.1%Tween]] | *[[McClean: PBS/0.1%Tween| PBS/0.1%Tween]] | ||
*[[McClean: Phosphate Buffered Saline| Phosphate Buffered Saline (PBS, 10x)]] | *[[McClean: Phosphate Buffered Saline| Phosphate Buffered Saline (PBS, 10x)]] | ||
*[[McClean: Potassium Phosphate | Potassium Phosphate Buffer]] | |||
*[[McClean: SeventyPercent_EtOH | Seventy Percent (70%) Ethanol]] | *[[McClean: SeventyPercent_EtOH | Seventy Percent (70%) Ethanol]] | ||
*[[McClean: TAE_50X | TAE Buffer (50X)]] | *[[McClean: TAE_50X | TAE Buffer (50X)]] | ||
*[[McClean: TE_10x | TE Buffer (10X)]] | *[[McClean: TE_10x | TE Buffer (10X)]] | ||
*[[McClean: Tris_Buffer | Tris Buffer]] | *[[McClean: Tris_Buffer | Tris Buffer]] | ||
*[[McClean: Yeast glycerol | Yeast Glycerol 30%]] | |||
*[[McClean:Chloramphenicol | Chloramphenicol]] | |||
*[[McClean:Kanamycin | Kanamycin]] | |||
==Microfluidics== | ==Microfluidics== | ||
*[[McClean: ConA | Concanavalin A Solution for Microfluidics]] | *[[McClean: ConA | Concanavalin A Solution for Microfluidics]] | ||
*[[McClean: Flow Cells | Constructing Flow Cells]] | *[[McClean: Flow Cells | Constructing PDMS Flow Cells]] | ||
*[[McClean: FCS2 for Cycling | FCS2 chamber for Metabolic Cycling]] | *[[McClean: FCS2 for Cycling | FCS2 chamber for Metabolic Cycling]] | ||
*[[User:Bohao Liu/Notebook/Research| Bandwidth Experiments]] | *[[User:Bohao Liu/Notebook/Research| Bandwidth Experiments]] | ||
*[[McClean: BioptechsTempExp | Bioptechs Temperature Experiments]] | |||
==Microscopy== | ==Microscopy== | ||
*[[McClean: Intro to the microscope| Introduction to the microscope]] | |||
*[[McClean: Microscope Dos and Don'ts| Microscope Dos and Don'ts]] | *[[McClean: Microscope Dos and Don'ts| Microscope Dos and Don'ts]] | ||
*[[McClean: Nikon_TI_Basic_Use | Nikon TI Basic Use]] | *[[McClean: Nikon_TI_Basic_Use | Nikon TI Basic Use]] | ||
| Line 128: | Line 159: | ||
*[[McClean: Quickie ImageJ Quantification | Quickie ImageJ Quantification]] | *[[McClean: Quickie ImageJ Quantification | Quickie ImageJ Quantification]] | ||
*[[McClean: NikonTI-Eclipse Setup and operation using Micromanager|NikonTI-Eclipse Setup and operation using Micromanager]] | *[[McClean: NikonTI-Eclipse Setup and operation using Micromanager|NikonTI-Eclipse Setup and operation using Micromanager]] | ||
*[[McClean: CleaningTheCamera| Cleaning the Camera's Cover]] | |||
==Equipment Maintenance== | ==Equipment Maintenance== | ||
| Line 142: | Line 174: | ||
*[[McClean:Annealing Oligos | Annealing Oligos]] | *[[McClean:Annealing Oligos | Annealing Oligos]] | ||
*[[McClean:Oligonucleotide phosphorylation, Annealing and Ligation | Oligonucleotide phosphorylation, Annealing and Ligation]] | *[[McClean:Oligonucleotide phosphorylation, Annealing and Ligation | Oligonucleotide phosphorylation, Annealing and Ligation]] | ||
*[[McClean:BlueLightSetup]] | *[[McClean:BlueLightSetup | How to Connect Blue LED to a Power Source, Parts and Instructions]] | ||
*[[McClean:InstallKappa |Compiling Kappa in a Linux environment]] | |||
<!--MM Added 10/24/2013 | <!--MM Added 10/24/2013 | ||
Revision as of 13:41, 22 February 2017
Back to McClean Lab
Basics
- Lab Expectations
- Lab Rules
- Lab Jobs
- Joining the Lab
- Leaving the Lab
- Lab Notebooks
- Dilution of Oligos
- Ordering Media
- Ordering Supplies
- Protocol Template
- Lab Database
- Lab Organization Notes
Introductory Exercises
Health and Safety
General Lab Procedures
- Washing Glassware
- Dry Ice-Ethanol Bath
- Pouring Gels for Electrophoresis (Mike)
- Using the Nanodrop2000
- Quantifying DNA with the Qubit Fluorometer
- Ordering Liquid N2 for Common Lab
Yeast
- Drug Concentrations
- Basic Chemostat Guide
- Bayanus Transformation
- Cleaning Floating Pin Replicators
- Fluorescence in situ Hybridization (Colin)
- Fluorescent in situ Hybridization (Ping)
- Fluorescent in situ Hybridization (Gasch Lab Collaboration)
- Fixation of Yeast (Bisaria Protocol)
- Fixation of Yeast (McClean Protocol)
- Fixation of Yeast (P. Xu Protocol)
- Frogging a Serial Dilution
- Frogging Tetrads
- Genomic DNA Prep (Bust 'n' Grab Protocol)
- GEV Strain Construction
- Glycerol stocks (yeast)
- Hemacytometer protocol for yeast
- Making and Using Frozen Yeast Competant Cells
- Mating Type Testers
- Phluorin Calibration
- Pinning (96 or 384 format)
- Plasmid Loss Assay
- Random Spore Prep
- Sanger Sequencing
- Smartstat Startup
- Sporulation
- Tetrad Dissection
- URA Pop-out
- Yeast Dubious ORFs
- Yeast Mating Halo Assay
- Yeast Nomenclature
- Yeast Recombinational Cloning
- Yeast Transformation (S. cerevisiae)
- YMC Induction in Chemostat
- Zygote Picking
- Working with the LoxP/Cre System in S. cerevisiae
- Western Blot
- Membrane Stripping
- Membrane Stripping-Mild
- Invasive growth assay
Bacteria
- Transformation of E. Coli
- E. coli Glycerol Stocks
- E. coli Competent Cells
- Colony PCR (E. coli)
- E. coli Electroporation
- Plasmid Prep from E. coli using a Qiagen Kit
PCR
- Designing Primers (Yeast)
- Colony PCR (Yeast)
- dNTP Stocks
- Touchdown PCR
- Takara PrimeStar PCR
- Anneal and Extend
- Designing "Yeast Toolkit" compatible primers
Other DNA Manipulations
Flow Cytometry
- General Flow Cytometry Procedure
- Cycloheximide Concentration Assay
- Flourecent Protein Folding Time Assay
- Induction time course
- Phase Plane Mapping
Media
- KS Amino Acid Supplement
- LB1
- LB2
- Low Fluorescence Media
- Low Fluorescence Agar Membranes
- Magic Marker Medias
- Quickie YPD supplemented with Adenine
- Synthetic Complete (SC) Yeast Media
- Synthetic Complete (SC) Media w/Drugs
- Synthetic Complete (SC) Media w/Canavanine
- YNB1
- YNB2
- YNB3
- YNB4
- YPD2
- YPD4
- Chloramphenicol media
- Kanamycin media
- 5FOA
Stock Solutions
- Agarose for gels
- α-Factor 1mg/ml Stock
- Bacterial Glycerol 65%
- Carbenicillin Stock Solution
- Concanavalin A Solution without ions
- Cycloheximide Stock Solution
- DNA Ladder Stock for PCR
- EDTA (0.5M)
- Geneticin/G418 Stock Solution
- Glucose Solution for Media
- PBS/0.1%Tween
- Phosphate Buffered Saline (PBS, 10x)
- Potassium Phosphate Buffer
- Seventy Percent (70%) Ethanol
- TAE Buffer (50X)
- TE Buffer (10X)
- Tris Buffer
- Yeast Glycerol 30%
- Chloramphenicol
- Kanamycin
Microfluidics
- Concanavalin A Solution for Microfluidics
- Constructing PDMS Flow Cells
- FCS2 chamber for Metabolic Cycling
- Bandwidth Experiments
- Bioptechs Temperature Experiments
Microscopy
- Introduction to the microscope
- Microscope Dos and Don'ts
- Nikon TI Basic Use
- Registering objectives on the Nikon
- 96 Well Plate Assay
- NIS Elements Repair
- New Scope Settings
- Quickie ImageJ Quantification
- NikonTI-Eclipse Setup and operation using Micromanager
- Cleaning the Camera's Cover
Equipment Maintenance
Misc
- 96 Well Plate Print Out
- AddGene Orders
- Blue Light Overview
- Sequencing
- Bibtex4Word (Add-in for word that allows you to use your existing BibTeX database)
- Orders from IDT/Genewiz/Macrogen/GenScript
- Searching a Sequence for All Database Primers
- Annealing Oligos
- Oligonucleotide phosphorylation, Annealing and Ligation
- How to Connect Blue LED to a Power Source, Parts and Instructions
- Compiling Kappa in a Linux environment
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