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Sam White
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Sam White

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Dan noticed that the computer wouldn’t boot, so I looked into it a bit. When attempting to boot, the hard drive (HDD) was making a clicking noise; this is never a good sign. I replaced the HDD with a clone of the existing (now dead) HDD that I had created…
Dan noticed that the computer wouldn't boot, so I looked into it a bit. When attempting to boot, the hard drive (HDD) was making a clicking noise; this is never a good sign. I replaced the HDD with...
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Sam White

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We were previously approached by Cindy Lawley (Illumina Market Development) for possible participation in an Illumina product development project, in which they wanted to have some geoduck tissue and DNA on-hand in case Illumina green-lighted the use of…
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Sam White

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Yesterday, I downloaded the Illumina FASTQ files provided by Genewiz for Hollie Putnam’s reduced representation bisulfite geoduck libraries. However, Genewiz had not provided a checksum file at the time. I received the checksum file from Genewiz and have…
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Sent the following samples to Illumina for possible selection in a new pilot sequencing platform they’re working on. The 12 samples will be used for RNAseq for genome annotation – numbers indicate desired sequencing priority. Juvenile and larval samples…
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Sam White

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Hollie Putnam asked me to help her get samples ready for submission for Illumina sequencing at Genewiz. She had previously prepared reduced representation bisulfite libraries on 20161215. She also prepped a whole genome library on 20161201 – specifically…
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Sam White

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After completing the downloads of these files from BGI, I needed to verify that the downloaded copies matched the originals. Below is a Jupyter Notebook detailing how I verified file integrity via MD5 checksums. It also highlights the importance of doing…
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Sam White

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Sent 10μg of the geoduck gDNA I isolated earlier today to Illumina on dry ice via FedEx Standard Overnight service.
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One of the long-running goals I’ve had is to get this Oly GBS data taken care of and out the door to publication. I think I will finally succeed with this, with the help of Pub-A-Thon. Don’t get too excited, it’s not what you think. It is not the drinking…
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Sam White

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Hollie Putnam prepared some reduced representation bisulfite Illumina libraries and had them sequenced by Genewiz. The data was downloaded and MD5 checksums were generated. IMPORTANT: MD5 checksums have not yet been provided by Genewiz! We cannot verify…
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Sam White

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We were approached by Cindy Lawley (Illumina Market Development) yesterday to see if we’d be able to participate in some product development. We agreed and need some geoduck DNA to send them, in case she’s able to get our species greenlighted for use.…
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Sam White

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Submitted 10μg (30.7μL) of the O.lurida gDNA I isolated on 20161214 to the UW PacBio facility – Order #450. Sequencing will be 10 SMRT cells. Turnaround time is ~7-8 weeks for UW customers (UW customers get queue priority).
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In an attempt to improve upon the partial genome assembly we received from BGI, we will be sending DNA to the UW PacBio core facility for additional sequencing. Isolated DNA from mantle tissue from the same Ostrea lurida individual used for the BGI…
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Introduction
I like playing video games and eating Kraft macaroni & cheese w/hotdogs.  Oh, and I also like Phish!
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