Not That Kind Of Worm Wiki



Welcome to the Not That Kind Of Worm Wiki
This is a wiki to share our lab protocols for what we do with C. elegans worms. We use these worms to study aging (somatic and reproductive) and zinc (and other metal) homeostasis.

These are our lab-specific protocols. General ones can be found on wormbook

General Worm Protocols

 * Freezing Worm Strains
 * How to find L4s VIDEO

General Molecular Biology Protocols

 * Worm lysis and PCR genotyping
 * RNA extraction protocol
 * RNA extraction protocol (Ciro 2016)
 * cDNA conversion
 * qPCR
 * worm CRISPR
 * Making cool-growth chemically competent E. coli
 * Restriction Enzyme List
 * Other Enzymes List

Measuring Worms

 * Using LEICA scope and WormSizer (PC)
 * Using LEICA scope and WormSizer (Mac)
 * Using LEICA scope with SD card
 * Micrometer Conversions for Zeiss compound scope
 * listed on the wall of the scope room for now


 * Growth and Reproduction Assay (for pop model project)


 * Filtration for stages

Software

 * Microscope image quantification: FIJI (FIJI is just ImageJ) is essential.
 * Editing photos: GIMP and IrfanView (or purchase Photoshop)
 * Making posters and figures: InkScape (or purchase Illustrator)
 * Sequence and Plasmid files: ApE (or purchase Sequencher, available on our shared MAC)
 * Statistics: R (or purchase GraphPad Prism)
 * Citations Manager: Mendeley (or purchase EndNote or Papers3)

Statistics

 * Handbook of Biological Statistics (here-are-my-data-which-test-do-I-use?)
 * An R Companion for the Handbook of Biological Statistics
 * R Basics Workshop (teach-yourself R)
 * R is good for Excel users
 * Wash U R Resources
 * A very quick introduction to ggplot in R
 * Should I use a t-test?
 * A: probably not.
 * unless you only have two groups in your x-variable (e.g. wt and mutant), a continuous numeric y-variable (e.g. worm length), and have confirmed normality and equal variances.
 * You can do an ANOVA online.
 * The Tukey post-hoc compares every group to every other group (e.g. wt & daf-2, wt & eat-2, eat-2 & daf-2).
 * If you want to only compare to the control, do it in Graphpad Prism, R, or another software with a Dunnett post-hoc.
 * Fisher's exact test online.
 * For categorical x-variable (wt and mutant), categorical y-variable (e.g. Fertile vs Sterile), with counts in each box (a contingency table)
 * Other statistical tests online.
 * for those people not comfortable using GraphPad Prism, Matlab, R, or another software.
 * For point-and-click lifespan analysis in R, can use OASIS
 * P-value errors
 * Please don't misuse bar graphs
 * Nature statistical checklist PDF

Scientific Writing

 * The Science of Scientific Writing PDF
 * Strunk and White Elements of Style Amazon PDF or ask any MGG grad student

Reproductive Aging Methods

 * Feeding fluorescent beads
 * Oil-Red-O

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