Sam’s Notebook: DNA Quality Assessment – Agarose Gel and NanoDrop on C.bairdi gDNA

I isolated C.bairdi gDNA yesterday (20200108) and now want to get an idea if it’s any good (i.e. no contaminants, high molecule weight).

I loaded ~100ng (2uL) of the _C.bairdi_ 20102558-2729 gDNA sample, along with two molecular weight markers (see RESULTS below) on a 0.8% agarose, 1x low TAE gel with ethidium bromide. Gel was run for 1.5hrs at 75V.

Sam’s Notebook: Lab Maintenance – Cluster UPS Battery Replacement

Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.

Bad battery indicator light:

APC UPS bad battery indicator light

Sam’s Notebook: DNA Isolation and Quantification – C.bairdi gDNA from EtOH Preserved Tissue

I isolated gDNA from ethanol-preserved C.bairdi muscle tissue from sample 20102558-2729 (SPNO-ReferenceNO). This sample was chosen as it had 0 in the SMEAR_result and BCS_PCR_results columns, indicating it should be free of Hematodinium. See the sample spreadsheet linked below for more info.

C.bairdi ethanol-preserved sample sheet from Pam Jensen (GoogleSheets):

I performed four separate isolations using 50mg of tissue. Samples were “ground” * in liquid nitrogen (LN2) with ceramic mortar/pestle and then processed using the E.Z.N.A. Mollusc DNA Kit according to the manufacturer’s protocol, with the following notes/changes:

  • Used ThermoFisher Proteinase K (18mg/mL) instead of that supplied by kit. Kit Proteinase K was moldy (!); the kit is nearly four years old…
  • Lysed tissue for 1hr.
  • Eluted with 200uL for each sample and pooled for final total volume of ~800uL.

Sample was quantified on the Robert Lab Qubit 3.0 using the DNA Broad Range assay, using 1uL of sample.

*The tissue did not powder as one would expect when grinding in liquid nitrogen. Instead, despite all utensils being pre-chilled with LN2 and tissue being actively ground under LN2, the tissue became a frozen paste that adhered to the pestle. I’ve never experienced this before, but I also have not attempted to grind ethanol-preserved tissue in LN2 before.