Wed. May 15, 2019 Salmon-sea lice salinity x temp methylomes

gDNA quality from yesterday’s extractions

0.8% agarose 1x TAE (low EDTA) 0.5ug/mL EtBr, 90min. @ 100V

Lanes:

Row 1:

  1. GeneRuler high range ladder 500ng
  2. empty
  3. 16C_32psu (1) 404ng (*stabbed the side of the well so some leaked out during loading)
  4. empty
  5. 16C_32psu (2) 344ng
  6. empty
  7. 16C_32psu (3) 418ng
  8. empty
  9. 16C_32psu (4) 436ng
  10. empty
  11. 8C_32psu (5) 346ng
  12. empty
  13. 8C_32psu (6) 308ng
  14. empty
  15. 8C_32psu (7) 344ng (bubble in well made some sample leak out)
  16. empty
  17. 8C_32psu (8) 306ng
  18. empty
  19. 8C_26psu (9) 314ng
  20. GeneRuler high range ladder 500ng

Row 2:

  1. GeneRuler high range ladder 500ng
  2. 8C_26psu (10) 368ng
  3. 8C_26psu (11) 333ng
  4. 8C_26psu (12) 395ng
  5. empty
  6. 16C_26psu (13) 362ng
  7. 16C_26psu (14) 386ng
  8. 16C_26psu (15) 309ng
  9. 16C_26psu (16) 315ng
  10. empty
  11. empty
  12. empty
  13. empty
  14. empty
  15. empty
  16. CTRL_8C_26psu (17) 432ng
  17. CTRL_8C_26psu (18) 484ng
  18. CTRL_16C_26psu (19) 420ng
  19. CTRL_16C_26psu (20) 433ng
  20. GeneRuler high range ladder 500ng

After 90 min. dye front ~3/4 to the bottom of the gel. Kind of hard to tell, but you can see faint purple right above the red plastic towards the bottom.

Ladder:

Because I ran a 0.8% the separation of high molec. weight wasn’t really great, but it was enough to see that most of the DNA is above the 4th ladder band (15KB) which is great!

There is definitely some degradation () but it’s not too bad.

It’s probably possible to remove small molec. weight DNA with beads, but not sure if it’s worth trying to clean these samples up and how these small fragments might affect the data.

Written on May 15, 2019