RNA and DNA Extractions for ENCORE Project, January 18, 2023

Protocol Link

Extraction of 12 samples from ENCORE Project. These samples were collected in Bermuda in August 2022 for the ENCORE TPC project. There are 160 samples total from the following 3 species: Diploria labyrinthiformis (DLAB), Montastraea cavernosa (MCAV), and Madracis decactis (MDEC) from the following temperatures 16, 22, 26, 29, 33, and 36 ºC (excluding 40 ºC for now)

Samples

Continuing on with the rest of the ENCORE extractions.

Notes

• Followed protocol exactly. Took 300 uL from the sample tubes for all species before proceeding with the extraction as written.

Qubit Results

• Used Broad range dsDNA and RNA Qubit Protocol
• All samples read twice, standard only read once

DNA Standards: 189.16 (S1) & 20760.08 (S2)

colony_id	Species	Temp.Cat	DNA_QBIT_1	DNA_QBIT_2	DNA_QBIT_AVG
Dlab-A1	Diploria labyrinthiformis	29	4.16	4.26	4.21
Dlab-A3	Diploria labyrinthiformis	33	4.38	4.34	4.36
Dlab-F1	Diploria labyrinthiformis	29	2.26	2.28	2.27
Mcav-B4	Montastraea cavernosa	16	7.82	7.66	7.74
Mcav-D6	Montastraea cavernosa	26	2.1	2.08	2.09
Mcav-E4	Montastraea cavernosa	16	6.76	6.72	6.74
Mcav-E5	Montastraea cavernosa	22	nd	nd	0
Mcav-F6	Montastraea cavernosa	26	3.28	3.22	3.25
Mdec-B1	Madracis decactis	29	5.08	4.86	4.97
Mdec-C3	Madracis decactis	33	4.34	4.34	4.34
Mdec-E7	Madracis decactis	36	26.8	26.6	26.7
Mdec-F4	Madracis decactis	16	7.4	7.32	7.36

RNA Standards: 414.76 (S1) & 9063.17 (S2)

colony_id	Species	Temp.Cat	RNA_QBIT_1	RNA_QBIT_2	RNA_QBIT_AVG
Dlab-A1	Diploria labyrinthiformis	29	12.4	12.8	12.6
Dlab-A3	Diploria labyrinthiformis	33	11.6	11.4	11.5
Dlab-F1	Diploria labyrinthiformis	29	nd	nd	0
Mcav-B4	Montastraea cavernosa	16	16.8	17.4	17.1
Mcav-D6	Montastraea cavernosa	26	11.4	11.4	11.4
Mcav-E4	Montastraea cavernosa	16	12.2	11.8	12
Mcav-E5	Montastraea cavernosa	22	11.4	11.4	11.4
Mcav-F6	Montastraea cavernosa	26	nd	nd	0
Mdec-B1	Madracis decactis	29	13	13.6	13.3
Mdec-C3	Madracis decactis	33	12.4	12.4	12.4
Mdec-E7	Madracis decactis	36	26.2	26	26.1
Mdec-F4	Madracis decactis	16	22.2	22	22.1

DNA and RNA Quality Check: Gel, using Kristina’s gel protocol at the bottom of this page.

Next steps

Will continue on with the rest of the extractions for these 3 species at these temps! Still holding off on the Porites astreoides extractions until we can find a suitable protocol. Also holding off on the 40 ºC temp for now, but will try to extract one or so from each species next week to see how it goes (not expecting much since the tissue was sloughing off of the corals at that temperature).