Sam's Notebook » qsonica http://onsnetwork.org/kubu4 University of Washington - Fishery Sciences - Roberts Lab Thu, 08 Nov 2018 21:47:12 +0000 en-US hourly 1 http://wordpress.org/?v=4.0 DNA Sonication & Bioanalzyer – C. virginica gDNA for MeDIP http://onsnetwork.org/kubu4/2017/12/11/dna-sonication-bioanalzyer-c-virginica-gdna-for-medip/ http://onsnetwork.org/kubu4/2017/12/11/dna-sonication-bioanalzyer-c-virginica-gdna-for-medip/#comments Mon, 11 Dec 2017 23:24:21 +0000 http://onsnetwork.org/kubu4/?p=2956

I transferred 8ug (136uL) of Crassotrea virginica gDNA (isolated earlier today) to two separate 1.7mL snap cap tubes for sonication/shearing.

I performed shearing at the NOAA Northwest Fisheries Science Center, using the Qsonica Q800R. Mackenzie Gavery assisted me.

Target fragment size was ~500bp.

Samples were run at the same time with the following settings:

  • 10 minutes
  • 30 seconds on, 30 seconds off
  • 25% power

After sonication, fragmentation was assessed using the Seeb Lab’s Bioanlyzer 2100 (Agilent) and the DNA 12000 Chip Kit (Agilent). NOTE: All of the reagents and the chips were past their expiration dates (most in June 2016).

Results:

Agilent 2100 Bioanalyzer Expert file (XAD): 2100 expert_DNA 12000_DE72902486_2017-12-11_13-45-31.xad

Fragmentation was successful, and pretty consistent.

Both samples appear to have an average fragment size of ~420bp. Will proceed with MeDIP, once reagents are received.

Unsheared gDNA:

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