DNA Technologies Core

DNA_logo_bannerThe mission of the DNA Technologies Core at the UC Davis Genome Center is to provide DNA analytical services to campus and other researchers.  We are currently focused on Next-Gen Sequencing (NGS) and genotyping, using mainly Illumina (HiSeq 3000, HiSeq 2500 and MiSeq), PacBio (RSII), and Fluidigm (C1-single cell analysis and Access Array) platforms. Our goal is to enable access to high throughput genome-wide analyses at economical recharge rates, as a functional extension of your laboratory. The services offered by the Genome Center complement other UC Davis facilities in order to provide access to numerous technologies for genomic analysis.

Read more about Getting Started in the Cores.

Services and Equipment

 

Technology Platforms Facility Services
Illumina Sequencing HiSeq 3000, HiSeq 2500 & MiSeq
PacBio Sequencing PacBio RSII
Fluidigm C1 Single Cell Genomics Auto-Prep
Fluidigm Access Array Target Amplification
Infinium Genotyping
Fluidigm EP1 Genotyping
Next-Gen Sequencing (Illumina and PacBio)
Next-Gen Library Prep
DNA Quantification/Library QC
Single Cell Genomics
Genotyping
Expression Analysis
Equipment: Training & Access
Sample QC: Agilent Bioanalyzer, Nanodrop, Caliper LabChip GX
Sample Prep: Covaris E220, Diagenode Bioruptor & Bioruptor NGS, Sage BluePippin
Automated Library Prep: Caliper Sciclone G3, IntegenX Apollo 324, Fluidigm Access Array

News

  • RNA-Seq Workshop – Library Preparation and Introduction to Data Analysis – August 9th to 11th 2017

    May 12, 2017
    August 9th, 9 a.m. – August  11th,  5 p.m. RNA-seq has revolutionized the way we address complex biological questions, allowing for differential gene expression, differential transcript analysis, as well as transcriptome assemblies. As sequencing output rapidly increases and sample numbers increase, library preparation becomes one of the major bottlenecks. This workshop provides comprehensive hands-on training in the preparation ...
  • Another Update on the Barcode Mis-Assignment Issue: Illumina’s White Paper

    April 19, 2017
    Illumina published a white paper today on the barcode mis-assignment issue (Illumina calls it somewhat euphemistically “barcode hopping”). In contrast to the Sinha et al. paper, which only presented data for libraries with NextSeq adapter sequences, the white paper shows that the issue is also relevant for TruSeq style adapters. The conclusions are fairly similar to the ones drawn in ...
  • Update on Barcode Mis-Assignment Issue

    April 11, 2017
    A “much-tweeted” manuscript was recently published on Biorxiv, investigating the barcode mis-assignment issues affecting HiSeq 3000, 4000, and HiSeq X, reported in our last newsletter.  Please see the manuscript here: Sinha et al. 2017  http://biorxiv.org/content/early/2017/04/09/125724 . As mentioned previously in our newsletter, the problem potentially affects low genome coverage sequencing studies and especially studies looking for low abundance mutations. The ...
  • April News: High-Throughput Gene-Expression Analysis – Index mis-assignments on HiSeq – NextSeq sequencing – Pippin HT library size selection

    April 6, 2017
    New High-Throughput Gene-Expression Analysis Services (3’Tag-Seq) The DNA Technologies and the Bioinformatics Cores have been working for more than half a year with a simplified RNA-Seq protocol that promises to drastically reduce the costs of many gene-expression studies, while fully maintaining the precision of the analysis. The new approach is called 3’Tag-Seq (or TagSeq, 3’Tag-RNA-Seq, Digital RNA-seq but these names have ...
  • PacBio Sequel Version 2 Chemistry and new Iso-Seq Protocol

    March 9, 2017
    PacBio Sequel Version 2 Chemistry   We have recently beta-tested the new PacBio Sequel chemistry (V2).  The tests have demonstrated significant yield and read-length improvements.  All current and future Sequel runs will be carried out with the new chemistry.  In addition to the V2 chemistry change, the Sequel software has been updated and allows now for 10 ...
  • Open between the holidays

    December 15, 2016
    We will be open before, after, and between the holidays and closed only on official UC holidays. The UC holidays are Friday the 23rd, Monday the 26th, Friday the 30th, and Monday the 2nd. Happy Holidays! The DNA Tech Core Staff.
  • Seminar: Simultaneous “multi-omic” measurement of gene fusions, mRNA, & proteins at 800-plex using single-molecule optical barcodes

    November 11, 2016
    Please joins us for the seminar: Simultaneous “multi-omic” measurement of gene fusions, mRNA, & proteins at 800-plex using single-molecule optical barcodes. Thursday, December 1st:  2pm to 3 pm Genome Center Auditorium (GBSF, #1005) Refreshments provided. Please RSVP using this link. ABSTRACT The ability to measure changes to DNA, RNA, and protein is crucial to developing a comprehensive understanding of biology in the genomics era. NanoString ...
  • New Service: Long-Read Sequencing on the PacBio Sequel

    November 10, 2016
    Pacific Biosciences (PacBio) has recently published a high quality de novo genome assembly for Arabidopsis based on the data of only two Sequel SMRT-cells. The Sequel is the second generation PacBio sequencer and generates up to 7x more reads per SMRT-cell compared to the first generation PacBio RSII sequencer. The DNA Technologies Core is now ...
  • RNA-Seq Workshop – Library Preparation and Introduction to Data Analysis – February 8th to 10th 2017

    October 27, 2016
    February 8th, 9 a.m. – February  10th,  5 p.m. RNA-seq has revolutionized the way we address complex biological questions, allowing for differential gene expression, differential transcript analysis, as well as transcriptome assemblies. As sequencing output rapidly increases and sample numbers increase, library preparation becomes one of the major bottlenecks. This workshop provides comprehensive hands-on training in the preparation of ...
  • RNA-Seq Workshop – Library Preparation and Introduction to Data Analysis – November 15th to 17th

    September 27, 2016
    We are sorry the workshop is fully booked. To subscribe to the our email list which announces the workshops, send an email to sympa@ucdavis.edu with the following information in the subject line: subscribe dnatech_news first_name last_name November 15, 2016, 9 a.m. – November 17, 9 a.m. to 6 p.m. RNA-seq has revolutionized the way we address complex biological questions, allowing for differential gene ...