DNA Technologies & Expression Analysis Cores

The DNA TECHNOLOGIES and EXPRESSION ANALYSIS CORES at the Genome Center provide high-throughput sequencing (also called Next Generation Sequencing, NGS), genotyping, and microarray analyses services as well as training and consultation services. Our goal is to enable access to high throughput genome-wide analyses at economical recharge rates, as a functional extension of your laboratory.

We offer the two major complementary sequencing technologies: Illumina sequencing and PacBio (long read) sequencing. For both technologies we provide the full spectrum of sequencing options and a wide range of sequencing library prep services. Genotyping is performed on a Fluidigm EP1 for low to medium assay numbers and Illumina Infinium arrays for high density array SNP genotyping. Gene expression analysis is carried out by RNA-seq on HiSeq sequencers and on Illumina Expression BeadChip arrays. Single-cell transcriptome and genome analyses are enabled by our Fludigm C1 instrument generating cDNA or whole genome amplifications from up to 96 individual cells.

We offer annual Illumina and PacBio sequencing library preparation workshops, consultations and custom sequencing library prep solutions.  The core equipment (with exception of the sequencers and the genotyping systems) is available to scientists on campus as Shared Equipment for a small usage fee.

We are operating one PacBio RSII, one Illumina HiSeq3000, one Illumina HiSeq2500, three MiSeq, liquid handling robots (IntegenX’s Apollo and Caliper/PerkinElmer’s Sciclone NGS G3), a Covaris E220 sonicator for high-throughput sample preparation, and Fluidigm Access Array & C1 single cell auto prep station. We maintain a LIMS that allows users fast access to sequence data.

Please see the page on how to get started with sequencing and genotyping at the Cores, and our FAQs. Please contact us at dnatech@ucdavis.edu for any remaining questions.

Our neighbors from the Bioinformatics Core provide sequence data analysis, statistical evaluations, consulting, and training to help you get the most out of your data. Please contact us for joint consultations with the Bioinformatics Core staff and also for complete analysis packages including sequencing and bioinformatics (e.g. differential gene expression, variant calling).

Our Services Include:

Sequencing library preps and associated services:

  • PacBio long insert DNA sequencing and Iso-Seq RNA sequencing library preparations
  • Illumina sequencing library preps:
  • Genomic DNA library preps
  • RNA-Seq library preps (poly-A enrichment or ribo-depletion)
  • High-Throughput (HT) library preps (DNA or RNA; starting from 24 libraries)
  • miRNA-Seq library preps
  • Methyl-seq: WGBS (Whole Genome Bisulfite Seq) and RRBS (Reduced Representation Bisulfite Seq)
  • Reduced representation library preps (e.g. for  genotyping by sequencing)
  • Mate Pair library preps
  • Library preps from ChIP samples
  • Library pooling
  • Nucleic acid QC (from single samples to 96-well plates)
  • Nucleic acid and library quantification
  • BluePippin nucleic acid size selection

Pleas see the GETTING STARTED  page to learn how to work with our Cores.

Our Shared Equipment includes:

  • Bioanalyzer – microcapillary nucleic acid fragment analysis for sample and library QC.
  • Caliper LabChip GX – a “high-­throughput bioanalyzer” (1-­‐384 samples).
  • Caliper Sciclone G3 – liquid handler robot for high-throughput library preps (up to 96 samples at at a time).
  • Covaris E220 – high-­throughput sonicator (1-­‐96 samples).
  • Diagenode Bioruptor sonicator
  • Diagenode Megaruptor – long insert size DNA shearing for PacBio library preps.
  • BluePippin – 50 bp to 50 Kb DNA automated size selection.
  • Fluidigm Access Array – target amplification for sequencing-­‐ready library prep.
  • Fluidigm C1 Single Cell Auto Prep – single cell transcriptome analysis and whole genome analyses.
  • FilterMax F5 Plate Reader – DNA/RNA quantification
  • Nanodrop – microvolume DNA/RNA quantification

Pleas see this SHARED EQUIPMENT page to learn how to get trained.