Samples for DNA methylation are from the pH experiment with shallow and mesophotic Stylophora pistillata adults. The DNA was extracted by me with the Zymo Quick-DNA/RNA Miniprep Plus Kit, following the protocol of emmastrand.

For this Methyl-Binding Domain Enrichment I used the protocol of meschedl with some adjustments.

Shearing Samples to ~500bp

1. Prepare samples for 1µg in 80µl of Tris HCl, see protocol Tris HCl

Sample	Volume DNA	Volume Tris HCl
S1	16.03	63.97
S2	18.25	61.75
S3	18.25	68.48
S4	36.9	43.1
S5	43.29	36.71
S6	58.82	21.18

1. For shearing the samples, I used the sonicator that they have in the biology department building.

Note: with their sonicator you can do only one sample at a time. Each sample was in a 1.5 ml tube.

1. Set time for 1min 30 sec, 30 second on 30 seconds off, 20% amplitude
2. Check samples on tapestation after sonication

MBD Enrichment

Made 43000µl of 1X Wash/Bind buffer from 5X concentrate before starting

Preparing Beads

1. Pipetted up and down the Dynabeads M-280 Streptavidin to resuspend them
2. Made 6 1.5mL tubes, each with 10µl of Dynabeads (the amount recommended for less than or equal to 1µg of DNA input)
3. Brought volume up to a total of 100µl with 90µl of 1X bind/wash buffer to each tube
4. Pipetted to mix
5. Placed tubes on long magnet rack and removed and discarded supernatant when clear
6. Removed tubes from rack and resuspended beads in 100µl 1X bind/wash buffer
7. Placed tubes on long magnet rack and removed and discarded supernatant when clear
8. Removed tubes from rack and resuspended beads in 100µl 1X bind/wash buffer

Coupling MBD-Biotin Protein to the Beads

1. Thawed MBD-Biotin protein from -80 on ice
2. Made 6 new 1.5mL tubes, each with 7µl of MBD-Biotin protein (amount recommended for 1µg of DNA input)
3. Added 93µl of 1X bind/wash buffer to each tube to get up to a total of 100µl
4. Transferred diluted protein to the washed bead tubes for a total volume of 200µl in each of 2 tubes
5. Put samples on the rotisserie mixer for 1 hour at room temp

Washing MBD-Biotin-Coupled Beads

1. Spun down briefly tubes from above
2. Placed tubes on magnet rack for 1 minute
3. Removed supernatant when clear
4. Resuspended beads in 100µl 1X bind/wash buffer and pipetted to mix
5. Mixed beads on rotisserie mixer for 5 minutes at room temp
6. Repeated: Spun down tubes briefly
7. Placed tubes on magnet rack for 1 minute
8. Removed supernatant when clear
9. Resuspended beads in 100µl 1X bind/wash buffer and pipetted to mix
10. Mixed beads on rotisserie mixer for 5 minutes at room temp
11. Repeated again: Spun down tubes briefly
12. Placed tubes on magnet rack for 1 minute
13. Removed supernatant when clear
14. Resuspended beads in 100µl 1X bind/wash buffer and pipetted to mix
15. Mixed beads on rotisserie mixer for 5 minutes at room temp
16. Finally: Spun down tubes briefly
17. Placed tubes on magnet rack for 1 minute
18. Removed supernatant when clear
19. Resuspended beads in 100µl 1X bind/wash buffer and pipetted to mix

Capture Reaction

1. To 6 new 1.5mL tubes, added 20µl each of 5X bind/wash buffer
2. To each appropriate tube, added the 80µl of the sheared DNA samples (above)
3. Transferred all of each diluted DNA sample to separate tubes with the MBD-Biotin bound beads for a total of 200µl in each tube and pipetted to mix
4. Mixed on rotisserie mixer overnight at 4 degrees C

Removing Non-Captured DNA

1. Again started by writing out protocol to calculate how much 1X bind/wash buffer to dilute (25000µl needed and appropriately diluted)
2. Took tubes out of the cold room rotisserie and spun down briefly
3. Placed tubes on magnet rack for 1 minute
4. Removed clear supernatant and SAVED in tubes labeled non-captured DNA and sample number
5. Resuspended beads in 200µl of 1X bind/wash buffer and placed on rotisserie mixer for 3 minutes
6. Spun down tubes briefly
7. Placed tubes on magnet rack for 1 minute
8. Removed clear supernatant and SAVED in tubes labeled wash and the sample number
9. Repeated: added 200µl 1X bind/wash buffer and placed on rotisserie mixer for 3 minutes
10. Spun down tubes briefly
11. Placed tubes on magnet rack for 1 minute
12. Removed clear supernatant and SAVED in the same tubes labeled wash and the sample number for a total of 400µl in each tube

Single Fraction Elution

1. Resuspended beads in 200µl each High Salt Elution buffer
2. Incubated on rotisserie mixer for 3 minutes
3. Spun down tubes breifly and placed on magnet rack for 1 minute
4. Removed supernatant when clear and SAVED in a new 1.5mL tube labeled captured DNA and the sample number
5. Repeated: added 200µl High Salt Elution Buffer to resuspended beads in each tube
6. Incubated tubes on rotisserie mixer for 3 minutes
7. Spun down tubes briefly and placed on magnet rack for 1 minute
8. Removed clear supernatant and SAVED in each sample tube for captured DNA, for a total of 400µl in each tube

Ethanol Precipitation

Each tube for ethanol precipitation gets 1µl of glycogen (co-precipitator), 1/10th the volume of the sample of 3M sodium acetate pH 5.2, and 2 volumes of the sample 100% ethanol:

Sample	vol glycogen (µl)	vol sodium acetate (µl)	vol 100% EtOH (µl)
S1 Captured	1	40	800
S2 Captured	1	40	800
S3 Captured	1	40	800
S4 Captured	1	40	800
S5 Captured	1	40	800
S5 Captured	1	40	800

1. Vortexed to mix and spun down
2. Placed tubes in the -80 freezer for 3.5 hours
3. Set centrifuge to 1 degrees C with about 15 min time left and let it run to get down to temp
4. Put 70% EtOH in -20 to chill down
5. Took sample tubes out of -80 and centrifuged for 15 minutes at 1 degrees C and 14,000 rcf
6. Took tubes out of centrifuge one at a time to keep cold, looked at tubes to see if there was a pellet. The non-captured 1431 sample did not have a visible pellet. In all these steps tubes were taken out of the centrifuge one at a time to keep them cold
7. Removed the supernatant and discarded very carefully. All samples had a very very small visible pellet
8. Added 500µl of cold 70% EtOH to each tube carefully
9. Centrifuged for 5 minutes at 1 degrees C and 14,000 rcf
10. Very carefully removed supernatant from pellet
11. Centrifuged tubes for 5 minutes at 1 degrees C at 14,000 rcf
12. Removed any remaining supernatant as best as possible with the smallest pipette tip and making sure to not removed the pellet
13. Air dried pellet for 3 minutes
14. Resuspended pellets in 25µl of ultra pure water
15. Check the DNA concentration with Nanodrop.

This protocol was followed by the Library preparation from the enriched methylated DNA fraction.