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Manually Clustering Immune Genes

Previously, we created files of transcripts that matched GO terms related to immune response. However, to make our steps more logically consistent, we recently changed those files to only include transcripts that matched the specific GO term (GO:0006955) for Immune Response. We created files for each of our three transcriptomes - cbai_transcriptomev2.0 (unfiltered), cbai_transcriptomev4.0 (bairdi only), and hemat_transcriptomev1.6 (hematodinium only). That was done using this script [Read More]

Immune Genes

A week or so ago, we decided to investigate a possible alternative path. Until now, we have generally been examining all genes. However, we decided that it may be interesting to look specifically at a subset in detail. Precisely, we decided to examine expression of immune genes among all individual libraries to see if we could spot any patterns. [Read More]

Manual Modules 4

Back in mid-July, I manually created modules to cluster genes by expression patterns. Again, “manual” oversells it a bit - I really just provided a cut height, looked at the resulting clusters, and then named them by overall expression patterns. A recap of that naming system can be found in my lab notebook entry on 2021-07-12 (named Manual Modules 3) [Read More]

Crab Plasticity

In our previous post, we created PCAs for each transcriptome, with each point as one library. This raised some interesting questions, notably that we didn’t necessarily see libraries from the same crab clustered together (though for some crab, they did clearly cluster). This could be an indication of crab plasticity, as they adjust to both tank effects and the temperature treatment. [Read More]