RNA and DNA Extractions for ENCORE Project, April 25, 2023

Protocol Link

Extraction of 16 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, 36, and 40 ºC

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.
• The DLAB DNA and RNA concentrations have been consistenly low but the quality is good. Eluted all DLAB DNA in RNA in 50 uL instead of 100 uL.

Qubit Results

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

DNA Standards: 198.48 (S1) & 22919.01 (S2)

colony_id	Species	Temp.Cat	DNA_QBIT_1	DNA_QBIT_2	DNA_QBIT_AVG
Dlab-D5	Diploria labyrinthiformis	22	4.24	5.28	4.76
Dlab-E1	Diploria labyrinthiformis	29	6.06	6.06	6.06
Mcav-A2	Montastraea cavernosa	40	23	23	23
Mcav-B5	Montastraea cavernosa	22	7.26	7.3	7.28
Mcav-D1	Montastraea cavernosa	29	7.62	7.58	7.6
Mcav-D2	Montastraea cavernosa	40	55.4	55.6	55.5
Mcav-F5	Montastraea cavernosa	22	3.2	3.18	3.19
Mdec-A1	Madracis decactis	29	2.88	2.98	2.93
Mdec-A2	Madracis decactis	40	28.4	28.4	28.4
Mdec-A3	Madracis decactis	33	6.26	6.38	6.32
Mdec-B4	Madracis decactis	16	4.4	4.46	4.43
Mdec-C1	Madracis decactis	29	8.52	8.6	8.56
Mdec-C7	Madracis decactis	36	19.6	19.6	19.6
Mdec-D2	Madracis decactis	40	22	22.4	22.2
Mdec-E2	Madracis decactis	40	11.4	11.5	11.45
Mdec-F3	Madracis decactis	33	4.72	4.8	4.76

RNA Standards: 423.98 (S1) & 8652.06 (S2)

colony_id	Species	Temp.Cat	RNA_QBIT_1	RNA_QBIT_2	RNA_QBIT_AVG
Dlab-D5	Diploria labyrinthiformis	22	13.8	14.2	14
Dlab-E1	Diploria labyrinthiformis	29	16.2	16.2	16.2
Mcav-A2	Montastraea cavernosa	40	17.2	17.2	17.2
Mcav-B5	Montastraea cavernosa	22	11.6	12	11.8
Mcav-D1	Montastraea cavernosa	29	14.4	14.6	14.5
Mcav-D2	Montastraea cavernosa	40	15.8	16	15.9
Mcav-F5	Montastraea cavernosa	22	10	10.4	10.2
Mdec-A1	Madracis decactis	29	6.9	6.6	6.75
Mdec-A2	Madracis decactis	40	22.6	23	22.8
Mdec-A3	Madracis decactis	33	15.8	15.6	15.7
Mdec-B4	Madracis decactis	16	15	15.6	15.3
Mdec-C1	Madracis decactis	29	26.2	26.4	26.3
Mdec-C7	Madracis decactis	36	21.2	21	21.1
Mdec-D2	Madracis decactis	40	21.6	21.8	21.7
Mdec-E2	Madracis decactis	40	17.4	17.6	17.5
Mdec-F3	Madracis decactis	33	15.4	16.2	15.8

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

Next steps

All done except for re-extractions!!!