Practice DNA/RNA Extractions of Larval Oyster Filters
Purpose: Extracting DNA and RNA from larval oyster samples from ARC1 and MV1 Vibrio challenges. Samples were chosen for practice based on the number of larvae preserved in each sample (see below).
Sample Description
| tube | sample | sample date | est # of larvae |
|---|---|---|---|
| 1 | ARC_T0_1 | 20230401 | 40,000 |
| 2 | ARC_T0_2 | 20230401 | 80,000 |
| 3 | MV1_CON_TV0 | 20230706 | 15,000 |
| 4 | MV1_STR_TV0 | 20230706 | 15,000 |
Larvae were collected onto Pluri filters, preserved with liquid nitrogen, stored in Whirlpaks and held in a -80 freezer until processing.
Using Zymo Quick-DNA/RNA Miniprep Plus Kit and DNA/RNA extraction protocol outlined in previous post.
QC results
Qubit
dsDNA Broad Range & RNA Broad Range (using 1 μL of sample)
| tube | sample | DNA_qubit_1 (ng/μL) | DNA_qubit_2 (ng/μL) | RNA_qubit_1 (ng/μL) | RNA_qubit_2 (ng/μL) |
|---|---|---|---|---|---|
| S1 | std1 | 352.78 RFU | 353.80 RFU | 86.21 RFU | - |
| S2 | std2 | 87661.85 RFU | 87742.50 RFU | 5657.86 RFU | - |
| 1 | ARC_T0_1 | 314 | 308 | too high | too high |
| 2 | ARC_T0_2 | 484 | 482 | too high | too high |
| 3 | MV1_CON_TV0 | 210 | 208 | 516 | 540 |
| 4 | MV1_STR_TV0 | 146 | 145 | 444 | 464 |
Gel
Ran 4 DNA samples on a gel with Amy (see labels)
TapeStation
Ran 4 RNA samples on TapeStation. Had to dilute the ARC samples 20:1 and the MV1_Vibrio samples 10:1.
Written on February 6, 2024