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protocols

This page contains the publicly available protocols developed to date with EDEN funding.

Some protocols were developed by EDEN exchange participants (graduate students, postdocs, or faculty). Other protocols were developed by undergraduate students who held EDEN summer internships (indicated with an asterisk *).

We hope to eventually make these protocols accessible via a searchable database. For now, they are simply grouped roughly into taxonomic groups based on the origanisms the protocols were designed for. Please browse through them to find ones that might be applicable to your work!

If you have protocols optimized for use in non-traditional organisms that you would be willing to make available here, please email them in PDF format to edenrcn@fas.harvard.edu with the subject line "Protocol."

 

Plant Protocols ** Vertebrate Protocols ** Invertebrate Protocols ** Other Protocols

Plant Protocols

Genetic transformation of bunchberry dogwood (Cornus canadensis) using Agrobacterium Suspension. Developed by Chris Trlica (North Carolina State University) during a summer internship in the Xiang lab.*

Spore germination and sex ration determination in moss. Developed by Tatum Norrell (University of Florida) during a summer internship in the McDaniel lab.*

Genetic transformation of moss (Ceratodon purpureus). Developed by Pierre-Francois Perroud of the Quatrano lab during an exchange visit to the McDaniel lab.

Estimating mesophyll conductance using combined gas exchange and chlorophyll fluorescence measurements. Developed by Christopher Muir of the Moyle lab during an exchange visit to the Galmes lab.

In Situ Hybridization in Plants. Developed by Fei Zhang of the Tadege Lab during an exchange visit to the Kramer Lab.

Making casts of flower parts for performing bumblebee preference tests. Developed by Veronica Di Stilio of the Di Stilio Lab during an exchange visit to the Glover Lab.

Experimental set up for performing bumblebee preference tests with movement (MOVIE). Developed by Veronica Di Stilio of the Di Stilio Lab during an exchange visit to the Glover Lab.

Bumblebee behavior with T. thalictroides plant (MOVIE). Developed by Veronica Di Stilio of the Di Stilio Lab during an exchange visit to the Glover Lab.

Transcriptome and morphological analyses in Selaginella apoda. Developed by Adam Geber (Columbia University) during a summer internship in the Ambrose Lab.*

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Vertebrate Protocols

Specimen preparation for magnetic resonance imaging (MRI) of stickleback (or other) fish. Developed by Jason Keagy of the Boughman lab during an exchange visit to the Braithwaite lab.

Pigeon in situ hybridization. Developed by Anna Vickrey (University of Utah) during a summer internship in the Shapiro lab.*

Stickleback (Gasterosteus) trypsin cleared alizarin and alican double stain. Developed by Brian Lohman (University of Idaho) during a summer internship in the Bell lab.*

Stickleback (Gasterosteus) whole-mount antibody staining with trypsin clearing. Developed by Brian Lohman (University of Idaho) during a summer internship in the Bell lab.*

Stickleback (Gasterosteus aculeatus) Whole-Mount Basket In Situ Hybridization. Developed by Linda Gai (Swarthmore College) during a summer internship in the Miller lab.*

Deer mouse (Peromyscus) spectrometry measurement and analysis of fur Brightness. Developed by Pavitra Muralidhar (Cornell University) during a summer internship in the Hoekstra lab.*

Specimen preparation (brain dissection and region extraction) for using RT-qPCR to examine gene expression in brain regions of a fish. Developed by Jessica Nowicki of the Pratchett Lab during an exchange visit to theO'Connell Lab.

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Invertebrate Protocols

Growing Archegozetes longisetosus Embryos De Mater. Developed by Austen Barnett of the Thomas lab during an exchange visit to the Schmidt-Ott lab.

Dissecting early-stage Embryos from Archegozetes longisetosus Adults. Developed by Austen Barnett of the Thomas lab during an exchange visit to the Schmidt-Ott lab.

Microinjecting Archegozetes longisetosus Embryos. Developed by Austen Barnett of the Thomas lab during an exchange visit to the Schmidt-Ott lab.

Microscopy techniques for Pelagia noctiluca embryos. Developed by Rebecca Helm of the Dunn lab during an exchange visit to the Gorsky lab.

Hydroides elegans culture, settlement assays and RNA isolation. Developed by Elizabeth Willsey (University of Toronto, Canada) during a summer internship in the Hadfield lab.*

Hydroides in situ hybridization protocol. Developed by Paul Bump (University of Hawaii, Manoa) during a summer internship in the Hadfield lab.*

Immunohistochemistry for cnidocytes and sensory neuron battery complexes in Hydractinia symbiolongicarpus. Developed by Atul Bhattarai (University of California, Davis) during a summer internship in the Grosberg lab.*

Embryo collection, cultivation, and gene silencing via zygotic RNAi in harvestman embryos. Developed by Prashant Sharma of the Giribet lab during an exchange visit to the Jockush lab.

One Color Section In Situ Hybridization for Octopus bimaculoides. Developed by Judit Pungor of the Thompson lab during an exchange visit to the Ragsdale lab.

B. anynana Crossing Scheme and Genomic DNA Extraction. Developed by Bethany Wasik of the Monteiro lab during an exchange visit to the Hoekstra lab.

B. anynana Double Digest Restriction-site Associated DNA (RAD)-Tag. Developed by Bethany Wasik of the Monteiro lab during an exchange visit to the Hoekstra lab.

Semi-high throughput measurement of hemoglobin concentration in Daphnia. Developed by Lev Yampolsky during an exchange visit to the Ebert lab.

Measurement of time until immobilization and time until the loss of heartbeat during acute exposure to high temperature in Daphnia. Developed by Lev Yampolsky during an exchange visit to the Ebert lab.

Nematostella vectensis genomic DNA preparation and Telomeric Restriction Fragment Analysis. Developed by Daniel Lackner of the Karlseder lab during an exchange visit to the Martindale lab.

Alcian blue staining for horseshoe crab (Limulus) Paraffin-Embedded Sections. Developed by Leslie Slota (University of Florida) during a summer internship in the Cohn lab.*

Immunohistochemistry for hyaluronic acid in horseshoe crabs (Limulus). Developed by Leslie Slota (University of Florida) during a summer internship in the Cohn lab.*

In situ hybridization on horseshoe crab (Limulus) Tissue Sections. Developed by Leslie Slota (University of Florida) during a summer internship in the Cohn lab.*

Horseshoe crab (Limulus) whole mount in situ hybridization. Developed by Leslie Slota (University of Florida) during a summer internship in the Cohn lab.*

Immunohistochemistry for tardigrade embryos (Hypsibius). Developed by Frank Smith of the Jockusch lab during an exchange visit to the Goldstein lab.

In situ hybridization for tardigrade embryos (Hypsibius). Developed by Frank Smith of the Jockusch lab during an exchange visit to the Goldstein lab.

Removal of tardigrade embryos (Hypsibius) from the maternal exuvium (MOVIE). Developed by Frank Smith of the Jockusch lab during an exchange visit to the Goldstein lab.

Eggshell removal from tardigrade embryos (Hypsibius) (MOVIE). Developed by Frank Smith of the Jockusch lab during an exchange visit to the Goldstein lab.

Blastomere ablations in amphipod (Parhyale) embryos. Developed by Frederike Alwes of the Extavour lab during an exchange visit to the Averof lab.

Making transgenic amphipods (Parhyale). Developed by Frederike Alwes of the Extavour lab during an exchange visit to the Averof lab.

Heat shock treatment for amphipods (Parhyale). Developed by Frederike Alwes of the Extavour lab during an exchange visit to the Averof lab.

In situ hybridization on snail embryos (Ilyanassa). Developed by Bishoy Kamel of the Medina lab during an exchange visit to the Lambert lab.

Making tools for manipulating slipper limpet embryos (Crepidula). Developed by Maryna Lesoway of the Collin lab during an exchange visit to the Henry lab.

Collection and fixation of slipper limpet embryos (Crepidula). Developed by Maryna Lesoway of the Collin lab during an exchange visit to the Henry lab.

In situ hybridization on slipper limpet embryos (Crepidula). Developed by Maryna Lesoway of the Collin lab during an exchange visit to the Henry lab.

Immunostaining on slipper limpet embryos (Crepidula). Developed by Maryna Lesoway of the Collin lab during an exchange visit to the Henry lab.

A calcium bioluminescence assay for functional analysis of mosquito (Aedes aegypti) and Tick (Rhipicephalus microplus) G Protein-coupled Receptors. Learned by Jeanne Serb of the Serb Lab during an exchange visit to the Pietrantonio Lab.

Protocol for growing algae and raising Amphioxus (Branchiostoma floridae). Developed by Tyler Square of the Muelemans Medeiros Lab during an exchange visit to the Yu Lab.

Whole mount in situ hybridization of imaginal disc of Trypoxylus dichotomus horn. Developed by Jema Rushe of theEmlen Lab during an exchange visit to the Niimi Lab.

Making casts of flower parts for performing bumblebee preference tests. Developed by Veronica Di Stilio of the Di Stilio Lab during an exchange visit to the Glover Lab.

How to Pick, Wash and Hatch Freshwater Sponge Gemmules. Developed by Quentin Schenkelaars of the Renard & Borchiellini Lab during an exchange visit to the Hill Lab.

Y27632 Treatment of Freshwater Sponge Gemmules. Developed by Quentin Schenkelaars of the Renard & Borchiellini Lab during an exchange visit to the Hill Lab.

RNAi on Freshwater Sponge Gemmules. Developed by Quentin Schenkelaars of the Renard & Borchiellini Lab during an exchange visit to the Hill Lab.

Sequencing mRNA from Cryo-Sliced Drosophila Embryos. Developed by Honghu Quan of the Lynch Lab during an exchange visit to the Eisen Lab.

In situ hybridization in Thermira biloba pupa. Developed by Kathy Su of the Meier Lab during an exchange visit to the Bowsher Lab.

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Other Protocols

Gibson Cloning. Developed by Anna Vickrey (University of Utah) during a summer internship in the Shapiro lab.*

Choanoflaggelate RNA extraction. Developed by Parinaz Fozouni (University of California, Berkeley) during a summer internship in the King lab.*

Cloning choanoflaggelate PCR products. Developed by Parinaz Fozouni (University of California, Berkeley) during a summer internship in the King lab.*

Tools for handling high-throughput sequence data. I. Cloud Computing with Amazon Web Services. Developed by Dacotah Melicher of the Bowsher lab during an exchange visit to the Dworkin lab.

Tools for handling high-throughput sequence data. II. Creating Storage Volumes For Large Files. Developed by Dacotah Melicher of the Bowsher lab during an exchange visit to the Dworkin lab.

Tools for handling high-throughput sequence data. III. Descriptions of Common Scripts and Workflow. Developed by Dacotah Melicher of the Bowsher lab during an exchange visit to the Dworkin lab.

Tools for handling high-throughput sequence data. VI. Quick and Effective Side-by-Side Installation of Linux on a Windows PC. Developed by Dacotah Melicher of the Bowsher lab during an exchange visit to the Dworkin lab.

How to use ImageJ with CASA plugin (Computer Assistant Sperm Analyzer). Developed by Charles Xu (University of Notre Dame) during a summer internship in the Hoekstra lab.*

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