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The Ness Lab Wiki

• Chlamydomonas information and protocols

  • Bold's carbenicillin plates
  • Bold's minimal medium recipe
  • Chlamydomonas Phenol-Chloroform DNA extraction
  • Chlamydomonas RNA extraction with Tri-Reagent
  • DNA Extraction: Chelex Method
  • DNA Extraction using Promega DNA Kit
  • Easy single colony isolation of vegetative cells
  • Freezing/Thawing protocol
  • Gel electrophoresis
  • How to grow Chlamy quickly in TAP
  • Multi-well plate templates
  • Mutation Accumulation Protocol
  • Natural Isolates/Strains
  • Neutral Lipid Methanol-Chloroform Extraction
  • PCR with Broad-Range,​C.reinhardtii-​specific Primers
  • Protocol for the sexual cycle in C. reinhardtii
    • Protocol to cyopreserve C. reinarhdtii
  • Quantify DNA concentration using Qubit
  • RNA Extraction with Maxwell RSC Plant RNA Kit (Promega)
  • Spin-free crosses
  • Standard Chlamydomonas reinhardtii PCR
  • Strains available in the lab (cryopreserved and/or on agar slants)
    • Ness Liquid Nitrogen Dewar
  • TAP(-N) Recipe

• Coding tips and tutorials

  • Bash Reference
  • BIO362: Learn Python through bioinformatics
  • cyvcf2 tutorial
  • Installing Python Packages on the Server Without Root Access
  • Installing R Packages on the Server Without Root Access
  • Intro to Awk

  • Making figures: ggplot examples

    • Bar plot
    • Making an ideogram / karyogram
    • Theme used for ggplot figures
    • X-Y scatterplot
  • Syncing GitHub repos on hpcnode1
  • Tips & Tricks for Efficient R Work
  • Useful .bash_profile settings

• Compute Canada

• File lists

• How-to articles
  • Nile Red Staining

• HPCnode 1 Documentation

  • Basic Project Structure
  • Connecting to the server
  • Connecting to the Server Using Windows
  • File Structure of HPCnode1
  • Switching to Anaconda2024
  • Getting started with Conda on HPCnode1
  • Getting the VPN
  • Important Files
  • Running Jupyter Notebooks on the server

• Lab supplies and ordering
  • Ordering supplies

• Projects

  • MA Expression
  • The effect of salt-stress on MA and adaptation
  • Wild Chlamy

• Teaching and Research Students

  • BIO481 marking scheme
  • ROP Marking Scheme