Extract DNA and RNA from 6 cod blood samples

[laurahspencer]

Cod blood samples for this test DNA + RNA extraction. I've provided 8 (4 each for treatment, 5C and 9C) in case any of these samples are missing or have very little blood.

Temperature	Sample #
5	129
5	149
5	154
5	155
9	84
9	93
9	111
9	114

[kubu4]

Alrighty, this is what we're looking at.

Here's notebook entry:

https://robertslab.github.io/sams-notebook/posts/2024/2024-08-29-DNA-and-RNA-Isolations---Gadus-macrocephalus-Blood/

Elution volumes were 15uL for DNA and 15uL for RNA.

---

• DNA Quantification (Google Sheet)

Sample_ID	Concentration(ng/uL)
84	12.5
93	3.42
111	18.3
114	58.8
129	0
149	20.8
154	7.76

---

• RNA Quantification (Google Sheet)

Sample_ID	Concentration(ng/uL)
84	18.6
93	28
111	22.8
114	20.6
129	7.9
149	22.2
154	21.8

---

I couldn't locate sample 155, BTW.

I think isolations could've been better. The blood coagulated into a dense goo as soon as I added the lysis buffer/proteinase k and didn't ever really break down. I probably should've tried to physically homogenize the samples after they lysis step showed minimal impact...

[sr320]

How are these quantities in terms of minimum for

RNA-seq and WGBS

[sr320]

@kubu4

How are these quantities in terms of minimum for

RNA-seq and WGBS

[kubu4]

Azenta's mimimum requirements:

Strand-specific RNA-seq: 500ng Ultra-low input RNA-seq: 20ng

WGBS: 500ng

Based on those numbers, we are short on all samples for Strand-specific RNA-seq and WGBS.

However, we could do the ultra-low input RNA-seq.

Additionally, there are many WGBS library kits that handle low input amounts of DNA (i.e. which we could process all of the DNA samples listed above).