Post bisulfite conversion samples from Previous Post hardly lost size at all, need to try again with a longer sonication.

Original sonication test tried 5 and 10 minute sonications, 10 minutes were much closer to 200-300 base pair ranges. This is what I tried with samples 221 and 1431 because there were more aliquots of 1µg ready for other shear tests.

Shearing Settings: 30 seconds on 30 seconds off pulse setting, amplitude 25%, and 10 minute time setting. Protocol for shearing was followed exactly.

Directly after shearing, samples were put into the Invitrogen Methylminer Methylated DNA Enrichment Kit. Because there were two samples again, exact steps from the previous post were followed, with the sample volumes.

Note: During wash of MBD beads pre-capture reaction one wash was longer than 5 minutes. Also time in -80 pre-precipitation was ~4 hours

After DNA re-suspension, HS Qubit was run, and samples pre and post enrichment were run on the D5000 TapeStation tape.

Qubit

Following High Sensitivity protocol

Sample	Standard 1 (RFU)	Standard 2 (RFU)	1st reading (ng/ul)	Second reading (ng/ul)	Average ng/ul
221 NC	64.87	24902	11.8	11.8	11.8
1431 NC	64.87	24902	34.2	34.2	34.2
221 W	64.87	24902	0.264	0.272	0.268
1431 W	64.87	24902	0.228	0.22	0.225
221 C	64.87	24902	1.19	1.18	1.18
1431 C	64.87	24902	0.736	0.722	0.730

TapeStation

Following D5000 protocol

Full results
Note last lane is something different and shouldn’t be considered

The “sizes” are larger in the captured peaks than the sheared, but I think that mostly has to do with inaccuracy at sizing something at such a low concentration.