Updates from the DNA Technologies Core Facility

Boreal Genomics Aurora DNA isolation/purification

We have added an Boreal Genomics Aurora instrument to our core for high quality DNA extraction and purification. The Aurora system enables the extraction DNA of high molecular weight DNA (up to megabase pair fragments) and the purification from difficult to remove contaminants. Please find more information on the Boreal Genomics website along with some example protocols.

UC Davis Genome Center Workshop on PacBio Sequencing and Data Analysis (Wet lab and Bioinformatics)

PacBio sequencing is the method of choice for de novo assembly of high quality genome sequences, the sequencing of long amplicons and complex repetitive regions, the analysis of gene isoforms, and structural variant detection. With support from Pacific Biosciences, we are offering a sequencing library preparation and data analysis workshop for this revolutionary technology — to our knowledge, the first such workshop worldwide. The library preparation workshop will take place on April 14–15th, 2015, at the UC Davis Genome Center. Hands-on data analysis using the PacBio SMRT-Portal will be explored on April 16th. The courses will begin at 8 am and end at 6 pm. To register, please use the workshop registration page. The library preparation workshop will cover the complete workflow starting from isolated DNA: sample QC, DNA shearing, library prep steps, library size selection and library QC. Libraries will be generated from genomic DNA samples. The participants will be able to work with their own sample and have the chance to generate a PacBio library, ready to sequence, for their research projects. Further, participants will be introduced to the details of the SMRT sequencing technology and other applications of the technology will be discussed. Participants will gain experience analyzing their PacBio sequencing reads using PacBio's SMRT-Portal software, via virtual machines running on Amazon Web Services (AWS). We will use both public example data, and reads obtained from the DNA Technologies Core's PacBio RS II, from libraries created during the workshop. Exercises will focus on running AWS virtual machines, data transfer and import, and assembly and variant finding protocols. Participants should be able to walk away from the workshop capable of analyzing their next PacBio data set independently. The registration fee for the three-day workshop is $500, which will include all workshop materials and lunches. The workshop will be limited to 10 participants. Attendees do not need to be affiliated with the UC Davis campus. To create the best possible libraries from your samples we highly suggest that you ship the samples at you earliest convenience to the DNA Technologies core for a QC of the DNA – we will run the sample on on a pulsed field electrophoresis gel. We will then inform you, if your sample will be suitable for PacBio sequencing. The DNA quality is essential for single molecule sequencing. We will provide control DNA samples in case you do not want to work with your own samples. For information on the sample requirements please see this page. Shipping instructions are also available.