Updates from the DNA Technologies and Expression Analysis Cores

This is an edited summary of the January Bulletin, the full version is available on the Expression Analysis Core website.

Whole genome sequencing for improved genome assemblies

The rapid progress of the sequencing technology and bioinformatics was demonstrated at the recent Plant and Animal Genome meeting in San Diego. For example the quality of de novo genome assemblies based on both Illumina and PacBio technologies have made major steps forward. Mammalian genome assemblies based on $10,000 sequencing efforts are reaching contig N50 metrics of 125 kb (employing PCR-free libraries, the Discovar assembler and 250 bp HiSeq reads) as demonstrated for a human genome.

New Services

HiSeq 250bp paired end sequencing

We are now running the new rapid chemistry (V2) which allows HiSeq sequencing with read lengths of up to 250 bp with paired end reads. When combined with PCR-free library preps (as offered by our core), these longer HiSeq data allow for Illumina based de novo genome assemblies of unprecedented quality.

High Throughput sequencing library prep services (DNA /RNA)

We are now offering at-cost high throughput library prep services for both DNA and RNA-seq libraries. The libraries are generated on our Caliper Sciclone robot. These services are customizable: for example some customers prefer to carry out sonications or library pooling themselves. We will keep on adjusting protocols to reduce costs as new technologies become available. One prerequisite for high throughput services is the submission of samples at homogeneous quality and concentrations in a 96 –well plate. The costs will also depend on the number and quality of samples. For example the complete costs for generating sequencing library pool for 96 samples from genomic DNAs would currently be $80 per sample (including: sonication, library prep, indexing, quantification and pooling into a single one pool). Please contact us to discuss details.

Methyl-seq — sequencing for epigenetic analyses

We now offer library preps and sequencing for DNA methylation analyses. This includes Whole Genome Bisulfite shotgun Sequencing (WGBS) as well as Reduced Representation Bisulfite Sequencing (RRBS).

Sonication — Covaris 96-well plates

We now have Covaris 96-well plates in stock (i.e 96-micro-glass-tube plates). These plates make the loading and unloading of the samples much more straightforward and faster as compared to the single tubes.

New PacBio Library Prep Workshop

With support from Pacific Biosciences we will be offering a PacBio library prep workshop in April. To our knowledge this might be the first such workshop worldwide. The Bioinformatics Core is planning to offer a one-day PacBio SMART-Portal data analysis bootcamp workshop on the day following our workshop. PacBio sequencing has gained tremendous importance in recent months because of the advantages of long-read information. Our hands-on workshop will focus on genomic DNA and long amplicon library preps and size selection. The workshops are tentatively scheduled for April 13th to 15th (PacBio library prep) and April 16th (SMRT-Portal bootcamp). Please email us (lfroenicke@ucdavis.edu or bioinformatics.core@ucdavis.edu) if you are interested and would like to be updated on the details as they become available. Please also bookmark the workshop page as the information will be updated.