Multi-omics analysis of thermal stress response in Aiptasia

Link to manuscript (Open Access in Proc. Royal Soc. B):

• http://rspb.royalsocietypublishing.org/content/285/1877/20172654 (HTML)
• http://rspb.royalsocietypublishing.org/content/285/1877/20172654.full.pdf (PDF)

Disclaimer

The title alludes to multiple -omics analysis--but a careful browser of this repository would notice that the stuff in here applies mainly to the PROTEOMIC bits of the project, with transcriptomic bits nowhere to be seen.

This is because the transcriptomics pipelines we used were... fairly standard (kallisto, sleuth). Our proteomics stuff weren't, therefore the scripts. Robert Frost's "The Road Not Taken" comes to mind here :p

Brief description of folder contents

Folders are ordered according to when it appears in the manuscript.

1. remove_duplicate_AIPGENEs/ explains how (and why) we excluded ~10% Aiptasia gene models from our analysis.
2. proteome_analysis/ is the folder that contains the giant Excel sheet that we used to carry out our proteome analysis.
3. proteome_glm/ was a GLM that we ran to check whether strain/temperature/a combination of both leads to significant changes in protein expression.
4. compare_abs_values/ contains scripts that led to plotting of Fig. 2.
5. compare_fc/ contains scripts that led to plotting of Fig. 3 and Fig. S1.
6. pick_representative_gene_models/... picks representative gene models to avoid bias in the downstream functional enrichment analysis.
7. rs_its2/ is how we analysed Symbiodinium types in our Red Sea Aiptasia.