McClean:Protocols: Difference between revisions
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*[[McClean: Lab Expectations | Lab Expectations]] | *[[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 19: | 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 26: | Line 28: | ||
*[[McClean: Nanodrop2000 | Using the Nanodrop2000]] | *[[McClean: Nanodrop2000 | Using the Nanodrop2000]] | ||
*[[McClean:Qubit | Quantifying DNA with the Qubit Fluorometer]] | *[[McClean:Qubit | Quantifying DNA with the Qubit Fluorometer]] | ||
*[[McClean: OrderingLiquidN2 | Ordering Liquid N2 for Common Lab]] | |||
==Yeast== | ==Yeast== | ||
| Line 34: | Line 37: | ||
*[[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 (McClean Protocol) | Fixation of Yeast (McClean Protocol)]] | ||
| Line 49: | 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: Sonication_Yeast | Sonication of Yeast]] | |||
*[[McClean: Sporulation | Sporulation]] | *[[McClean: Sporulation | Sporulation]] | ||
*[[McClean: Tetrad Dissection | Tetrad Dissection]] | *[[McClean: Tetrad Dissection | Tetrad Dissection]] | ||
| Line 82: | Line 87: | ||
*[[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== | ==Other DNA Manipulations== | ||
*[[McClean: Golden Gate-Making a new part | Golden Gate-Making a new part]] | *[[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 112: | Line 119: | ||
*[[McClean:Chloramphenicol media | Chloramphenicol media]] | *[[McClean:Chloramphenicol media | Chloramphenicol media]] | ||
*[[McClean:Kanamycin media | Kanamycin media]] | *[[McClean:Kanamycin media | Kanamycin media]] | ||
*[[McClean:5FOA | 5FOA]] | |||
==Stock Solutions== | ==Stock Solutions== | ||
Revision as of 16:48, 8 March 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
- Sonication of Yeast
- 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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