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Judelson Lab Protocols and Safety Documents

GENOMIC DNA AND RNA PREPS
P. infestans genomic DNA
Cleaning up genomic DNA using CTAB
RNA extraction from P. infestans

DNA CLONING AND ANALYSIS
Primer and oligonucleotide design strategies
Restriction digestion of DNA
Cloning and sequencing PCR products
Ligations and cloning
Colony disruption assay (rapid screening for inserts)
Cloning oligos into plasmids
Spotting DNA on filter paper (for storage or shipping)
Alkaline lysis E. coli DNA preps
E. coli boiling prep miniscreen
A-Tailing PCR products for cloning

MISCELLANEOUS BACTERIAL METHODS
Chemically competent E. coli cells
Electroporation of E. coli
Recovering bacteria from microtiter plate stocks
Making electrocompetent E. coli DH5-alpha (Eppendorf protocol)
Recycling electroporation cuvettes
Plating lambda libraries
Lambda plaque lifts

POLYMERASE CHAIN REACTION
Standard PCR (and colony PCR)
RAPD analysis
PCR amplification from phage plaques
Adding restriction sites using PCR: beware of methylation
SSCP analysis
RT-qPCR worksheet

MEDIA
Amsco autoclave instructions
General autoclaving guidelines
Chinese media (Xu's)
Lima bean media (ALBA)
Formaldehyde (RNA) gels
Rye and green pea media
Modified Plich media

HYBRIDIZATIONS AND GELS
General information on DNA gels and photo documentation
RNA gels (formaldehyde method)
Northern blots using glyoxal
cDNA probes from total RNA
Preparing glyoxal for RNA gels
Southern blotting of DNA (including making probes by random priming, and hybridization)
Hybridizations using an oligonucleotide as probe

PHYTOPHTHORA TRANSFORMATION
Phytophthora bombardment protocol
Phytophthora electroporation protocol (zoospores)
Protoplast transformation of P. infestans

MANIPULATIONS OF PHYTOPHTHORA
Preparing different developmental stages from P. infestans
Determining mating types
Harvesting sporulating and nonsporulating tissue
Making crosses and germinating oospores
Infecting leaflets with P. infestans
Freezing P. infestans in liquid nitrogen
How to keep a good laboratory notebook
Formaldehyde fixation for microscope

REPORTER ASSAYS
GUS staining (histochemical)
GUS assays (fluorometric)

USE OF LAB EQUIPMENT
Changing liquid nitrogen tanks
G-force and rpm conversions for rotors in lab
Removing photographic fixer stains from clothing
Centrifuge rotors: use and cleaning
How to use the Rainin Pipetman
Rainin's Pipetman guide (includes replacement part numbers)
Using the moticam on the microscope
Quick guide for use of Beckman spectrophotometer
Electrophoresis area policy
Performing ligations in the microcooler
Short instructions for Microfuge20

PROFESSIONAL DEVELOPMENT ITEMS
How to keep a good laboratory notebook
Advice on writing scientific papers
Learn a useful trade: how to wash glassware

SAFETY
Safety training document for Judelson lab
Wipe test instructions
Departmental Chemical hygiene plan
Departmental Injury and Illness Prevention Program
Flame and Alcohol SOP
Phenol SOP
Liquid nitrogen SOP
Formaldehyde SOP
Ethidium bromide SOP
Formaldehyde SOP
Acid handling SOP
Bleach SOP
Guidance on using bleach for decontamination
Handling of biological materials SOP
Microwave SOP

MISCELLANEOUS FORMS
Radioactivity request and log sheet
Log sheet for working in radioactivity area
Log sheet for equipment (2 hr slots)
Log sheet for working in transfer hood (1 hr slots)
Form for signing-out materials

Safety
last modified August, 2019

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