Newsletter, January 2015

UCD Genome Center – DNA Technologies and Expression Analysis Cores News Bulletin

Dear DNA Technologies Core users,
We hope the New Year is treating you well. To kick off the year, this newsletter will introduce a range of new services (250 bp read length Hiseq sequencing, High Throughput library preps, Methyl-seq, sonication), new workshops (PacBio), and provide updates on the core lab and sequencing developments.

UPDATES/NEWS

HiSeq replacement!
Our previous Hiseq 2500 sequencer had intermittent technical problems that occurred with increasing frequency. We re-ran affected lanes, but nevertheless the problems and the numerous Illumina repair attempts caused several delays for which we would like to apologize once more. The good news is that Illumina has replaced our previous Hiseq 2500 system. The new Hiseq system is working great with Illumina quality metrics considerably higher and consistent.

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 250pb reads on the Hiseq; please see below!) as demonstrated for a human genome. The results included even a 40 kb contig not present in the human reference. Last year groups presenting PacBio data titled their talks “Near perfect genome assemblies of ….. “ . This year the “Near” was omitted. For example the de novo assembly of the goat genome had a contig N50 of 5 Mb (PacBio data only). Also, another “better than reference” genome was announced for rice based on PacBio data.

NEW SERVICES

HiSeq 250bp paired end sequencing:
We are now running the new rapid chemistry (V2) which allows HiSeq sequencing with read length 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 (please see above).

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. One can, of course, use only the number of glass tubes needed and save the rest of the plate for future sonications. You must buy a complete plate though.

NEW WORKSHOPS

PacBio Library Prep workshop — PacBio SMRT Portal course:
With support of 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 work shop. PacBio sequencing has gained tremendous importance in recent months because of the advantages of long-read information (please see the NEWS section). 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 in one or both of the workshops 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.

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