McClean:Protocols: Difference between revisions
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==Introductory Exercises== | ==Introductory Exercises== | ||
*[[McClean: Intro_to_yeast | Introduction to Yeast]] | *[[McClean: Intro_to_yeast | Introduction to Yeast]] | ||
*[[McClean: Tester Protocol | Tester Protocol]] | |||
==Health and Safety== | ==Health and Safety== | ||
*[[McClean: Safety101 | Safety 101]] | *[[McClean: Safety101 | Safety 101]] | ||
*[[McClean: SharpsDisposal | | *[[McClean: SharpsDisposal | Sharps Disposal]] | ||
*[[McClean: OkToTrash | Ok to Trash Stickers]] | *[[McClean: OkToTrash | Ok to Trash Stickers]] | ||
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*[[McClean:Qubit | Quantifying DNA with the Qubit Fluorometer]] | *[[McClean:Qubit | Quantifying DNA with the Qubit Fluorometer]] | ||
*[[McClean: OrderingLiquidN2 | Ordering Liquid N2 for Common Lab]] | *[[McClean: OrderingLiquidN2 | Ordering Liquid N2 for Common Lab]] | ||
*[[McClean: Using the Klett | Klett protocols]] | |||
==Yeast== | ==Yeast== | ||
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*[[McClean: Frogging_Tetrads | Frogging Tetrads]] | *[[McClean: Frogging_Tetrads | Frogging Tetrads]] | ||
*[[McClean: Genomic DNA Prep (Bust 'n' Grab Protocol)| Genomic DNA Prep (Bust 'n' Grab Protocol)]] | *[[McClean: Genomic DNA Prep (Bust 'n' Grab Protocol)| Genomic DNA Prep (Bust 'n' Grab Protocol)]] | ||
*[[McClean:Genomic_DNA_prep_(LiAc_SDS_method)| Genomic DNA Prep (LiAc SDS method)]] | |||
*[[McClean: GEV Strain Construction | GEV Strain Construction]] | *[[McClean: GEV Strain Construction | GEV Strain Construction]] | ||
*[[McClean: Glycerol stocks (yeast) | Glycerol stocks (yeast)]] | *[[McClean: Glycerol stocks (yeast) | Glycerol stocks (yeast)]] | ||
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*[[McClean: Zygote Picking| Zygote Picking]] | *[[McClean: Zygote Picking| Zygote Picking]] | ||
*[[McClean: Working with the LoxP/Cre System in S. cerevisiae| Working with the LoxP/Cre System in S. cerevisiae]] | *[[McClean: Working with the LoxP/Cre System in S. cerevisiae| Working with the LoxP/Cre System in S. cerevisiae]] | ||
*[[McClean:EMSA Protocol| EMSA Protocol]] | |||
*[[McClean:Western Blot| Western Blot]] | *[[McClean:Western Blot| Western Blot]] | ||
*[[McClean:Membrane stripping|Membrane Stripping]] | *[[McClean:Membrane stripping|Membrane Stripping]] | ||
*[[McClean:Membrane_Stripping_Mild|Membrane Stripping-Mild]] | *[[McClean:Membrane_Stripping_Mild|Membrane Stripping-Mild]] | ||
*[[McClean:Invasive growth assay|Invasive growth assay]] | *[[McClean:Invasive growth assay|Invasive growth assay]] | ||
*[[McClean:Yeast_viability_with_methylene_blue|Methylene blue viability assay]] | |||
==Bacteria== | ==Bacteria== | ||
*[[McClean:Transformation of E. Coli | Transformation of ''E. Coli'']] | *[[McClean:Transformation of E. Coli | Transformation of ''E. Coli'']] | ||
*[[McClean:E. coli Glycerol Stocks | ''E. coli'' Glycerol Stocks]] | *[[McClean:E. coli Glycerol Stocks | ''E. coli'' Glycerol Stocks]] | ||
*[[McClean:Competent Cells| ''DH5alpha'' Competent Cells with Mix & Go kit (Renee)]] | |||
*[[McClean:Competent Cells| ''E. coli'' Competent Cells]] | *[[McClean:Competent Cells| ''E. coli'' Competent Cells]] | ||
*[[McClean:Colony PCR(E. coli) | Colony PCR (''E. coli'')]] | *[[McClean:Colony PCR(E. coli) | Colony PCR (''E. coli'')]] | ||
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*[[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]] | *[[McClean: Designing "Yeast Toolkit" compatible primers | Designing "Yeast Toolkit" compatible primers]] | ||
*[[McClean: Q5 Mutagenesis Kit from NEB | Q5 Mutagenesis Kit from NEB]] | |||
*[[McClean:Colony_PCR_(Quick_Load) | Colony PCR (Quick Load)]] | |||
== | ==Modular Cloning-Yeast Toolkit assembly== | ||
*[[McClean: Designing "Yeast Toolkit" compatible primers | Designing "Yeast Toolkit" compatible primers]] | |||
*[[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]] | *[[McClean: Golden Gate- Making a multi-part plasmid | Golden Gate-Making a multi-part plasmid]] | ||
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==Media== | ==Media== | ||
*[[McClean:Chloramphenicol media | Chloramphenicol media]] | |||
*[[McClean:Kanamycin media | Kanamycin media]] | |||
*[[McClean:KS Amino Acid Supplement | KS Amino Acid Supplement]] | *[[McClean:KS Amino Acid Supplement | KS Amino Acid Supplement]] | ||
*[[McClean:LB1 | LB1]] | *[[McClean:LB1 | LB1]] | ||
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*[[McClean:Magic Marker Medias | Magic Marker Medias]] | *[[McClean:Magic Marker Medias | Magic Marker Medias]] | ||
*[[McClean:QuickAdeYPD | Quickie YPD supplemented with Adenine]] | *[[McClean:QuickAdeYPD | Quickie YPD supplemented with Adenine]] | ||
*[[McClean:YPG | YPG]] | |||
*[[McClean:SC_Media | Synthetic Complete (SC) Yeast Media]] | *[[McClean:SC_Media | Synthetic Complete (SC) Yeast Media]] | ||
*[[McClean:SC_MediawDrugs | Synthetic Complete (SC) Media w/Drugs]] | *[[McClean:SC_MediawDrugs | Synthetic Complete (SC) Media w/Drugs]] | ||
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*[[McClean:YPD2 | YPD2]] | *[[McClean:YPD2 | YPD2]] | ||
*[[McClean:YPD4 | YPD4]] | *[[McClean:YPD4 | YPD4]] | ||
==Stock Solutions== | ==Stock Solutions== | ||
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*[[McClean: Alpha Factor Stock | α-Factor 1mg/ml Stock]] | *[[McClean: Alpha Factor Stock | α-Factor 1mg/ml Stock]] | ||
*[[McClean: Bacterial Glycerol 65%| Bacterial Glycerol 65%]] | *[[McClean: Bacterial Glycerol 65%| Bacterial Glycerol 65%]] | ||
*[[McClean: FISH ConA| Concanavalin A Solution without ions]] | *[[McClean: FISH ConA| Concanavalin A Solution without ions]] | ||
*[[McClean: Ladder_Stock_for_PCR | DNA Ladder Stock for PCR]] | *[[McClean: Ladder_Stock_for_PCR | DNA Ladder Stock for PCR]] | ||
*[[McClean: EDTA (0.5M) | EDTA (0.5M)]] | *[[McClean: EDTA (0.5M) | EDTA (0.5M)]] | ||
*[[McClean: Glucose Solution | Glucose Solution for Media]] | *[[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: Potassium Phosphate | Potassium Phosphate Buffer]] | ||
*[[McClean: Plasmid Prep Buffers | Generic recipes for Qiagen buffers]] | |||
*[[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)]] | ||
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*[[McClean: Tris_Buffer | Tris Buffer]] | *[[McClean: Tris_Buffer | Tris Buffer]] | ||
*[[McClean: Yeast glycerol | Yeast Glycerol 30%]] | *[[McClean: Yeast glycerol | Yeast Glycerol 30%]] | ||
==Drugs== | |||
*[[McClean:Drug Concentrations | Drug Concentrations]] | |||
===E.Coli=== | |||
*[[McClean:Carbenicillin Stock Solution | Carbenicillin Stock Solution]] | |||
*[[McClean:Chloramphenicol | Chloramphenicol]] | *[[McClean:Chloramphenicol | Chloramphenicol]] | ||
*[[McClean:Gentamicin | Gentamicin]] | |||
*[[McClean:Kanamycin | Kanamycin]] | *[[McClean:Kanamycin | Kanamycin]] | ||
*[[McClean:Spectinomycin | Spectinomycin]] | |||
===S.cerevisiae=== | |||
*[[McClean:5FOA | 5FOA]] | |||
*[[McClean:ClonNat | ClonNat]] | |||
*[[McClean: Cycloheximide Stock Solution| Cycloheximide Stock Solution]] | |||
*[[McClean: Geneticin/G418 Stock Solution | Geneticin/G418 Stock Solution]] | |||
*[[McClean:Hygromycin B | Hygromycin B]] | |||
==Microfluidics== | ==Microfluidics== | ||
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==Equipment Maintenance== | ==Equipment Maintenance== | ||
*[[McClean: Laboratory_Cabinet_Maint | Laboratory Cabinet Maintenance]] | |||
*[[McClean: RollerDrum_BrushReplacement | Roller Drum Brush Replacement]] | *[[McClean: RollerDrum_BrushReplacement | Roller Drum Brush Replacement]] | ||
*[[McClean: PlasmaPreen_ORingReplacement | Plasma Preen O-Ring Replacement]] | |||
*[[McClean: LowDiskSpace | Microscope #1 computer -- Low Disk Space Warning]] | |||
==Misc== | ==Misc== | ||
Latest revision as of 12:48, 5 February 2024
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
- Klett protocols
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)
- Genomic DNA Prep (LiAc SDS method)
- 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
- EMSA Protocol
- Western Blot
- Membrane Stripping
- Membrane Stripping-Mild
- Invasive growth assay
- Methylene blue viability assay
Bacteria
- Transformation of E. Coli
- E. coli Glycerol Stocks
- DH5alpha Competent Cells with Mix & Go kit (Renee)
- 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
- Q5 Mutagenesis Kit from NEB
- Colony PCR (Quick Load)
Modular Cloning-Yeast Toolkit assembly
- Designing "Yeast Toolkit" compatible primers
- Golden Gate-Making a new part
- Golden Gate-Making a multi-part plasmid
Flow Cytometry
- General Flow Cytometry Procedure
- Cycloheximide Concentration Assay
- Flourecent Protein Folding Time Assay
- Induction time course
- Phase Plane Mapping
Media
- Chloramphenicol media
- Kanamycin media
- KS Amino Acid Supplement
- LB1
- LB2
- Low Fluorescence Media
- Low Fluorescence Agar Membranes
- Magic Marker Medias
- Quickie YPD supplemented with Adenine
- YPG
- Synthetic Complete (SC) Yeast Media
- Synthetic Complete (SC) Media w/Drugs
- Synthetic Complete (SC) Media w/Canavanine
- YNB1
- YNB2
- YNB3
- YNB4
- YPD2
- YPD4
Stock Solutions
- Agarose for gels
- α-Factor 1mg/ml Stock
- Bacterial Glycerol 65%
- Concanavalin A Solution without ions
- DNA Ladder Stock for PCR
- EDTA (0.5M)
- Glucose Solution for Media
- PBS/0.1%Tween
- Phosphate Buffered Saline (PBS, 10x)
- Potassium Phosphate Buffer
- Generic recipes for Qiagen buffers
- Seventy Percent (70%) Ethanol
- TAE Buffer (50X)
- TE Buffer (10X)
- Tris Buffer
- Yeast Glycerol 30%
Drugs
E.Coli
S.cerevisiae
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
- Laboratory Cabinet Maintenance
- Roller Drum Brush Replacement
- Plasma Preen O-Ring Replacement
- Microscope #1 computer -- Low Disk Space Warning
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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