RNA and DNA Re-Extractions for ENCORE Project, April 27, 2023

Protocol Link

Re-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

16 re-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: 194.09 (S1) & 22253.03 (S2)

colony_id	Species	Temp.Cat	DNA_QBIT_1	DNA_QBIT_2	DNA_QBIT_AVG
Dlab-A6	Diploria labyrinthiformis	26	0	0	0
Dlab-A7	Diploria labyrinthiformis	36	3.32	3.46	3.39
Dlab-C6	Diploria labyrinthiformis	26	0	0	0
Dlab-D6	Diploria labyrinthiformis	26	0	0	0
Dlab-E4	Diploria labyrinthiformis	16	2.34	2.4	2.37
Dlab-E6	Diploria labyrinthiformis	26	0	0	0
Dlab-F1	Diploria labyrinthiformis	29	2.24	2.26	2.25
Dlab-F3	Diploria labyrinthiformis	33	0	0	0
Dlab-F4	Diploria labyrinthiformis	16	0	0	0
Dlab-F5	Diploria labyrinthiformis	22	2.18	2.26	2.22
Dlab-F6	Diploria labyrinthiformis	26	2.26	2.28	2.27
Mcav-B6	Montastraea cavernosa	26	2.38	2.42	2.4
Mcav-C6	Montastraea cavernosa	26	5.42	5.48	5.45
Mcav-F4	Montastraea cavernosa	16	5.6	5.62	5.61
Mcav-F6	Montastraea cavernosa	26	4.72	4.8	4.76
Mdec-D5	Madracis decactis	22	2.78	2.82	2.8

RNA Standards: 414.64 (S1) & 8566.59 (S2)

colony_id	Species	Temp.Cat	RNA_QBIT_1	RNA_QBIT_2	RNA_QBIT_AVG
Dlab-A6	Diploria labyrinthiformis	26	12	12	12
Dlab-A7	Diploria labyrinthiformis	36	11	11.4	11.2
Dlab-C6	Diploria labyrinthiformis	26	13.4	13.6	13.5
Dlab-D6	Diploria labyrinthiformis	26	11	11.6	11.3
Dlab-E4	Diploria labyrinthiformis	16	11	11	11
Dlab-E6	Diploria labyrinthiformis	26	0	0	0
Dlab-F1	Diploria labyrinthiformis	29	16	15.8	15.9
Dlab-F3	Diploria labyrinthiformis	33	12	11.6	11.8
Dlab-F4	Diploria labyrinthiformis	16	10.8	10	10.4
Dlab-F5	Diploria labyrinthiformis	22	11	10.4	10.7
Dlab-F6	Diploria labyrinthiformis	26	11.8	10.6	11.2
Mcav-B6	Montastraea cavernosa	26	12	11.4	11.7
Mcav-C6	Montastraea cavernosa	26	14.2	13.8	14
Mcav-F4	Montastraea cavernosa	16	18.6	17.8	18.2
Mcav-F6	Montastraea cavernosa	26	15.2	15.4	15.3
Mdec-D5	Madracis decactis	22	14.8	13.8	14.3

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

Next steps

All done except for pooling and plate prep!