ALL OF OUR METHODS CAN BE FOUND ON protocols.io
https://www.protocols.io/groups/collier-lab

Experimental
Breaking up clumps of cells using sonication
Electroporation of Aurantiochytrium

Growth and staining protocols
Growth medium for Labyrinthula
Acriflavine (for cell wall) either on a filter or by centrifugation
Nile Red (for lipids) in unfixed or fixed cells
Propidium iodide (for DNA)

Computational
Codon usage analysis code is available at protocols.io
-The raw codon usage output can be found at Academic Commons
Motifs near initiation codon (Kozak sequences)
Significance of secondary structure of predicted Kozak sequences.
Sequences matching yeast transcription factor binding motifs
-The raw output of the regulatory element motif search can be found at Academic Commons

 

These protocols were generated by J. Collier, J. Rest et al. as part of a grant from the Gordon and Betty Moore Foundation.