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Extract DNA from cod blood samples #1922

Open sr320 opened 3 weeks ago

laurahspencer commented 3 weeks ago

It looks like there is also some leftover gDNA from fin clips in the freezer at NOAA, which was used for lcWGS.

sr320 commented 1 week ago

@laurahspencer can you select blood samples that make sense based on treatment / RNA-seq - 8 coldest 8 warmest?

laurahspencer commented 1 week ago

Yes, I'll do so tomorrow. I'll also be at SAFS tomorrow, bringing fin clip tissue and/or DNA over from NOAA.

sr320 commented 3 days ago

@laurahspencer can you get a list of samples for extraction?

laurahspencer commented 3 days ago

Here I list 20 samples total - five each of blood and fin tissues from 0C and 16C. Blood samples are frozen, fin clips are in ethanol in the flammables hood. For fin clips, if there's sufficient tissue it'd be great to use only a portion of it for this sequencing effort.

Steven, in terms of funding, how many total samples can we do? If are you intending this to be a preliminary sequencing run, then we'd go back and do more depending on what we see I can pare back the list to fewer samples. If I were to choose a tissue to focus on, it would be fin clips since they are much easier to collect from fish. There could be issues with blood samples since we simply flash froze them, whereas other folks typically add anticoagulants and/or centrifuge them.

Also - we plan to throw a few jaw bone samples in there (currently in the process of getting them from folks at Newport), and a few sleeper shark fin and/or muscle samples will arrive in the mail in the next week or so, which we'll also need to process for methylation analysis similar to these samples.

Tube Label Sample # Tank Temp Treatment Tissue Type
39 B 39 12 0 Blood
47 B 47 11 0 Blood
50 B 50 11 0 Blood
59 B 59 10 0 Blood
70 B 70 9 0 Blood
4 B 4 1 16 Blood
11 B 11 2 16 Blood
12 B 12 2 16 Blood
18 B 18 3 16 Blood
30 B 30 4 16 Blood
39 F 39 12 0 Caudal Fin
47 F 47 11 0 Caudal Fin
50 F 50 11 0 Caudal Fin
59 F 59 10 0 Caudal Fin
70 F 70 9 0 Caudal Fin
4 F 4 1 16 Caudal Fin
11 F 11 2 16 Caudal Fin
12 F 12 2 16 Caudal Fin
18 F 18 3 16 Caudal Fin
30 F 30 4 16 Caudal Fin

To document why we're doing this- the idea is to look for temperature biomarkers in the epigenome, i.e. informative CpG sites for which methylation predicts temperature treatment. Blood and fin clips are good candidate tissues for biomarker development for this since they are non-invasive. The future aim would be to see if methylation levels at biomarker sites persist after the fish return to common temperatures. Here are a couple related studies- one in zebrafish that looked at this in gonad tissue (and also identified sex biomarkers), and one that used blood from chickens.