I was kind of all over the place after lunch running the DIG-PCR and finally working out the script for the sea urchin BLAST, but am happily ending the day searching spIDs for under-expressed adhesion proteins for the sea star transcriptomics project. While I felt a little scatterbrained with the RCN approaching and with the culmination of these projects looming, I’m happy to report two successes:
1) Monica and I successfully synthesized the DIG-probes for the candidate microbial pathogen today. After we ran the probe out on the gel we got a bright band right at 250bp. We have probe, and although one of our controls boiled off during the PCR, I ran another PCR synthesis after dinner and have that metaphorical bun in the oven. The plan is to move forward with the sea star ISH this Sunday as the RCN winds down, so we have time to pull data together for our speed talks.
2) I also finally was able to BLAST our transcriptome against the sea urchin nucleotide base from Spbase, but am only getting a fraction of homologous genes that should be there. Collin is also curious at the general characterization of our transcriptomic data, although he’s approaching it a little differently. According to Collin, the annotations we’re working with include a total of 3947 urchin genes (not necessarily significantly differentially expressed). I’m getting 782 genes (I think maybe my BLAST parameters are too stringent). Take a look at my notebook and let me know what you think (hint: the most interesting part is at the bottom).
Thank you Maya for the fun lecture and lab time on ecological modeling today!