What we did
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Followed Matt’s protocol (RNAzol and column extraction) to extract RNA from whole oysters (D4, D9, D12, D14 from MgCl control), except spun down RNA till there was nothing left in the water (no RNA on Qubit or nanodrop), so we resuspended the pellet and continued the protocol from there.
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Got a ton more RNA from redoing the second part, but contamination was bad. See results below.
| ID | RNA conc (ng/uL) | 260/280 | 260/230 |
|---|---|---|---|
| D4 | 878 | 1.98 | 1.73 |
| D9 | 950 | 1.91 | 1.62 |
| D12 | 296 | 1.73 | 1.35 |
| D14 | out of range | 1.90 | 1.79 |
Things I messed up (classic)
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Need to be more careful with oysters during initial tissue collection and homogenization. Could have definitely introduced some stuff there.
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Having talked to some molecular bio people in my cohort, the wash step we did may have not been enough/the wash step can bring in contamination somehow?