Tardigrade (Assignment 10) data outline

Tardigrade (Assignment 10) data outline

 

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Tardigrade transcriptomics

In your last two assignments, we are interested in performing our own transcriptomic analysis using a combination of Galaxy (to filter and map our reads) and R (to perform differential gene expression analysis). We have discovered that tardigrade species, which are a diverse group of animals with unique abilities to withstand extreme environmental conditions, differ in their developmental rates and life histories, which could ultimately affect the mechanisms by which they respond to external stimuli. A recent article we read studied the differences in gene expression across development between two tardigrade species, Hypsibius dujardini and Ramazzottius varieornatus.

 

Comparison of the transcriptomes of two tardigrades with different hatching coordination

https://bmcdevbiol.biomedcentral.com/articles/10.1186/s12861-019-0205-9

 

They included data from a previous publication that compared the genomes of these two species:

 

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002266

 

 

Answer these questions

 

  1. Choose which developmental stages to contrast (in both species). Tell me which 2 stages you chose.
  2. Choose two genes you will be tracking to see how they are expressed among the chosen stages. Tell me which genes these are – provide both gene names and their accession numbers in both species, and tell me your rationale behind choosing these two genes.
  3. What do you expect you will find in terms of gene expression among these stages and genes and why? Will they differ between species? What GO terms are associated with the genes you chose?

 

Some resources: https://www.ncbi.nlm.nih.gov/genome and http://ensembl.tardigrades.org/index.html

 

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