Tag Archives: Eastern oyster

Phenol:Chloroform Extractions and EtOH Precipitations – MspI Digestions of C.virginica DNA from Earlier Today

The two MspI restriction digestions from earlier today for our project with Qiagen were subjected to phenol:chloroform cleanup and subsequent ethanol precipitations.

Phenol:chloroform clean up procedure:

  1. Added equal volume (50μL) of phenol:chloroform:IAA (25:24:1) to each sample.

  2. Vortexed.

  3. Centrifuged 5mins, 16,000g at room temperature.

  4. Transferred aqueous phase (top layer) to clean 0.5mL snap-cap PCR tube.

  5. Added equal volume of chloroform (50μL) to aqueous phase.

  6. Vortexed.

  7. Centrifuged 5mins, 16,000g at room temperature.

  8. Transferred aqueous phase (top layer) to clean 0.5mL snap-cap PCR tube.

Performed ethanol precipitation on both samples according to lab protocol.

Resuspended precipitated DNA in 25μL Buffer EB (Qiagen).

Will quantify with Qubit 3.0.


Restriction Digestion – MspI on Crassotrea virginica gDNA

Digested two 1.5μg aliquots of Crassostrea virginica isolated 20171211, as part of the project we’re doing with Qiagen.

Digestion reactions:

Component Volume(μL)
DNA (1.5μg) 25.7
10x CutSmart Buffer (NEB) 5.0
Water 17.3
MspI (NEB) 2

MspI info:

  • NEB R0106T (100,000U/mL; rec’d 20171214)

Reactions were carried out in 0.5mL snap-cap PCR tubes and incubated for 15mins @ 37oC in a PTC-200 thermalcycler (MJ Research), no heated lid.

Samples will be subjected to a phenol:chloroform extraction for cleanup.


DNA Quantification – C.virginica MBD-enriched DNA

Quantified Crassostrea virginica MBD-enriched DNA from earlier today for Qiagen project.

Used the Qubit 3.0 (ThermoFisher) and the Qubit dsDNA Broad Range (BR) Kit (ThermoFisher).

Used 1uL of template DNA.


Quantification Spreadsheet (Google Sheet): 20180110_qubit_dsDNA_BR_MBD_virginica

Both samples had decent yields and have usable quantities for Qiagen (they wanted ~300ng from each sample):

virginica_MBD_01 – 18.3ng/uL (457.5ng = 5.7% methylated DNA capture)

virginica_MBD_02 – 19.6ng/uL (490ng = 6.1% methylated DNA capture)

Will store @ -20C until next week so that we’re not shipping so close to the weekend (shipping address is in Germany).


MBD Enrichment – Crassostrea virginica Sheared DNA Day 3

Continued MBD enrichment of C.virginica DNA from yesterday for Qiagen project.

Followed the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) manufacturer’s protocol for input DNA amounts of 1 -10ug (I am using 8ug in each of two samples).

Since the protocol has two elution steps that are each saved separately from each other for each sample, I did the following to combine the two elution fractions into a single sample:

  • Pelleted one elution fraction from each sample
  • Discarded supernatant from pelleted sample
  • Transferred second elution fraction to the pellet from the first elution fraction
  • Pelleted second elution fraction

The rest of the ethanol precipitation procedure was followed per the manufacturer’s protocol.

Final pellets were resuspended in 25μL of Buffer EB (Qiagen) and stored temporarily on ice for quantification.


MBD Enrichment – Crassostrea virginica Sheared DNA Day 2

Continued MBD enrichment for C.virginica and Qiagen project from yesterday.

Followed the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) manufacturer’s protocol for input DNA amounts of 1 -10ug (I am using 8ug in each of two samples).

Performed a single, high-salt elution.

Samples were precipitated O/N @ -80C.


MBD Enrichment – Crassostrea virginica Sheared DNA Day 1

As part of a project with Qiagen to have them try out some of our DNA with their newest DNA bisulfite conversion kit, I previously isolated DNA from Crassotrea virginica (Eastern oyster) and sheared to ~420bp.

Next, I needed to enrich the samples for methylated DNA. Did this using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen). Followed the manufacturer’s protocol for input DNA amounts of 1 -10ug (I am using 8ug in each of two samples). Below are the exact volumes used for various steps:

Made 1x Bind/Wash Buffer

  • 2.88mL 5x Bind/Wash Buffer

  • 720uL molecular biology grade H2O


  • 80uL beads per sample

MBD-biotion protein:

  • 56uL per sample

Diluted the two sheared DNA samples to 25ng/uL:

  • CiVi = CfVf
  • (58.4ng/uL)(136uL) = (25ng/uL)(Vf)

  • Vf = 317.7

  • Add 181.7uL H2O to DNA to get 317.7ul (i.e. 25ng/uL)

Samples were incubated O/N in the 4C in the rotator.


Tissue Sampling – Crassostrea virginica Tissues for Archiving

I figured it’d be prudent to collect some Eastern oyster (Crassotrea virginica) to have around the lab.

I used one of the C.virginica oysters that I picked up Taylor on 20171210 for sampling.


  • Upper mantle (avoided area that was near gonad/white-ish)
  • Ctenidia
  • Lower mantle
  • Muscle
  • Gonad

Samples were transferred to 1.7mL snap cap tubes, frozen on dry ice, and stored @ -80C in Rack 13, Col 1, Row 5.


DNA Sonication & Bioanalzyer – C. virginica gDNA for MeDIP

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).


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:


DNA Isolation & Quantification – Crassostrea virginica Mantle gDNA

DNA was isolated from a single adult Eastern oyster (Crassostrea virginica) for a pilot project with Qiagen to test their new DNA bisulfite conversion kit. The oyster was obtained yesterday afternoon (20171210) from the Taylo rShellfish Pioneer Square location. The oyster was stored @ 4C O/N.

The oyster was shucked and four pieces of upper mantle tissue (~35mg each) were snap frozen in liquid nitrogen (LN2). Tissues were pulverized under LN2 and then DNA was isolated separately from each sample using the E.Z.N.A. Mollusc DNA Kit (Omega) according to the manufcaturer’s protocol.

Samples were eluted with 100uL of Elution Buffer and were pooled into a single tube.

The gDNA was quantified using the Qubit 3.0 (Invitrogen) and Qubit dsDNA Broad Range Kit (Invitrogen), using 5uL of sample.


Qubit (Google Sheet): 20171211_qubit_virginica_DNA

Concentration is 58.4ng/uL.

That makes the total yield ~23.36ug (23360ng). This is more than enough to perform two separate MeDIP preps and two separate reduced representation digestions with MspI.

Will proceed with shearing of DNA for MeDIP.


Goals – May 2015

Here are the things I plan to tackle throughout the month of May:

Geoduck Reproductive Development Transcriptomics

My primary goal for this project is to successfully isolate RNA from the remaining, troublesome paraffin blocks that have yet to yield any usable RNA. The next approach to obtain usable quantities of RNA is to directly gouge tissue from the blocks instead of sectioning the blocks (as recommended in the PAXgene Tissue RNA Kit protocol). Hopefully this approach will eliminate excess paraffin, while increasing the amount of input tissue. Once I have RNA from the entire suite of samples, I’ll check the RNA integrity via Bioanalyzer and then we’ll decide on a facility to use for high-throughput sequencing.


BS-Seq Illumina Data Assembly/Mapping

Currently, there are two projects that we have performed BS-Seq with (Crassostrea gigas larvae OA (2011) bisulfite sequencing and LSU C.virginica Oil Spill MBD BS Sequencing) and we’re struggling to align sequences to the C.gigas genome. Granted, the LSU samples are C.virginica, but the C.gigas larvae libraries are not aligning to the C.gigas genome via standard BLASTn or using a dedicated bisulfite mapper (e.g. BS-Map). I’m currently BLASTing a de-novo assembly of the C.gigas larvae OA 400ppm sequencing that Steven made against the NCBI nt DB in an attempt to assess the taxonomic distribution of the sequences we received back. I’ll also try using a different bisulfite mapper, bismark, that Mackenzie Gavery has previously used and has had better results with than BS-Map.


C.gigas Heat Stress MeDIP/BS-Seq

As part of Claire’s project, there’s still some BS-Seq data that would be nice to have to complement the data she generated via microarray. It would be nice to make a decision about how to proceed with the samples. However, part of our decision on how to proceed is governed by the results we get from the two projects above. Why do those two projects impact the decision(s) regarding this project? They impact this project because in the two projects above, we produced our own BS-Seq libraries. This is extremely cost effective. However, if we can’t obtain usable data from doing the library preps in-house, then that means we have to use an external service provider. Using an external company to do this is significantly more expensive. Additionally, not all companies can perform bisulfite treatment, which limits our choices (and, in turn, pricing options) on where to go for sequencing.



When I have some down time, I’ll continue working on migrating my Wikispaces notebook to this notebook. I only have one year left to go and it’d be great is all my notebook entries were here so they’d all be tagged/categorized and, thus, be more searchable. I’d also like to work on adding README files to our plethora of electronic data folders. Having these in place will greatly facilitate the ability of people to quickly and more easily figure out what these folders contain, file formats within those folders, etc. I also have a few computing tips/tricks that I’d like to add to our Github “Code” page. Oh, although this isn’t really lab related, I was asked to teach the Unix shell lesson (or, at least, part of it) at the next Software Carpentry Workshop that Ben Marwick is setting up at UW in early June. So, I’m thinking that I’ll try to incorporate some of the data handling stuff I’ve been tackling in lab in to the lesson I end up teaching. Additionally, going through the Software Carpentry materials will help reinforce some of the “fundamental” tasks that I can do with the shell (like find, cut and grep).

In the lab, I plan on sealing up our nearly overflowing “Broken Glass” box and establishing a new one. I need to autoclave, and dispose of, a couple of very full biohazard bags. I’m also going to vow that I will get Jonathan to finally obtain a successful PCR from his sea pen RNA.