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WGBS planning for Pacific cod (and shark) #1935

Closed laurahspencer closed 2 months ago

laurahspencer commented 4 months ago

This is regarding the quote obtained for WGBS sequencing (#1732) .

For this sequencing run we plan to include DNA from a few different Pacific cod tissue types (blood, fin, jawbone). The blood and fin DNA is coming from our lab. The jawbone DNA probably needs to be sent from a different lab that specializes in bone DNA extraction. @kubu4 Can I have our collaborators ship jawbone DNA separately from their lab for sequencing?

We also plan to send a few samples from the Pacific sleeper shark, which probably has a very large genome (perhaps as large as 12Gb). Since this quote is for 12 GB/sample, this could result in low coverage. @kubu4 can the facility accommodate two species during library prep, and increase data for a few sleeper shark samples?

Just to triple check- we're sending DNA and they are doing the bisulfite treatment etc.?

kubu4 commented 4 months ago

Can I have our collaborators ship jawbone DNA separately from their lab for sequencing?

Certainly.

can the facility accommodate two species during library prep, and increase data for a few sleeper shark samples?

They can accommodate different species (it's just DNA), however, we'd likely need to get a separate quote for the sleeper shark samples.

we're sending DNA and they are doing the bisulfite treatment etc.?

Yes.

NOTE: I'm going to need to get a new quote. The old quote expired in April...

kubu4 commented 4 months ago

@laurahspencer - Please create a new issue with desired sequencing info for sleeper shark samples.

laurahspencer commented 4 months ago

Great, thanks!