Updates from the DNA Technologies and Expression Analysis Cores

The following announcements are taken from the April Newsletter from the DNA Technologies and Expression Analysis Core Facilities. Read the newsletter for full details.

Latest Generation Illumina HiSeq 3000 Sequencer now available

The Genome Center has acquired a HiSeq 3000 sequencer that provides faster sequencing at significantly reduced per-base-costs. The new sequencer is already delivered and will be installed this week and then tested. Please note that for some samples the library preps should be adjusted for the HiSeq 3000.The new sequencer is more than three times faster than the HiSeq 2500 and yields about 65% more reads per lane. For example the run-time of a paired-end 100 bp run is only 3 days on the HiSeq 3000 compared to 11 days on the HiSeq 2500. The number of reads per lane has improved from between 150–190 million (HiSeq 2500) to 260–310 million reads (HiSeq 3000). The maximum read length is 150 bp compared to 100 with the HiSeq 2500 High Output mode.In contrast to the X10, the HiSeq 3000 will sequence samples from all organisms. The flowcell is not appropriate for all types of libraries. For example the HiSeq 3000 system is not yet recommended for low-complexity sample sequencing (e.g. amplicons, GBS, or RAD-seq). A second limitation of the HiSeq 3000 is the restriction of library insert sizes to a max of about 500 bases (with average recommended insert size being 350bp or less). We can assist you in making your libraries HiSeq 3000 compatible.

The HiSeq Sequencing Queue Is Online

Details of the HiSeq sequencing calendar, as well as the sequencing queue, are now online at dnatech.genomecenter.ucdavis.edu/hiseq-calendar. You can track your order by the sample arrival data for a specific run type or email Charlotte for your project ID.

Fluidigm EP1 genotyping

We are currently testing the Fluidigm Juno system which integrates IFC and thermocycler. This system allows highly multiplexed genotyping from as little as 5.5 ng input DNA.