Mission: DNA Technologies & Expression Analysis Cores

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 4000, NextSeq, and MiSeq), PacBio (Sequel and RSII), and Fluidigm (C1-single cell analysis and Access Array) , and 10X Genomics Chromium platforms (linked-read genome sequencing). Our goal is to enable access to high throughput genome-wide analyses at economical recharge rates, as a functional extension of your laboratory.

expression_analysis_core_banner The mission of the Expression Analysis Core at the UC Davis Genome Center is to provide services and technologies for gene expression analyses at the genomic level. We are focused on exploiting high throughput sequencing. We offer standard as well as specialized and custom RNA-seq library prep services for Illumina sequencing. The PacBio Iso-Seq protocol enables full-length transcript sequencing and thus the discovery new gene isoforms.  The 10X Genomics Chromium single-cell platform allows single-cell and single-nuclei gene expression profiling for up to 10,000 cells or nuclei.
Workshops in these technologies are an important part of facility operations. We also offer access to liquid handlers and nucleic acid analyzers to facilitate your experiments.

Read more about Getting Started in the Core.

Services and Equipment

 

Technology Platforms Facility Services
Illumina Sequencing HiSeq 4000, NextSeq & MiSeq
PacBio Sequencing PacBio RSII, Sequel
10X Genomics Chromium   Single-Cell Gene Expression; Whole Genome Linked Reads
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 Science BluePippin, Pippin HT
Automated Library Prep: Caliper Sciclone G3, IntegenX Apollo 324, Fluidigm Access Array

News

  • Seminar: April 4th The Beacon Automated Single Cell Biology Platform

    March 30, 2018
    The Beacon Automated Single Cell Biology Platform Troy Lionberger, Ph.D., Sr. Manager, Technology Development, Berkeley Lights Davis Campus:              11 am, Wednesday April 4th;  Room 4202 GBSF/Genome Center Building Sacramento Campus:    1  pm  , Wednesday April 4th; Room 1241 MedEd building The Digital Cell Biology technology developed by Berkeley Lights allows scientists to: Process individual cells radically faster than other technologies Automate and scale workflows far beyond manual, ...
  • Single-Cell Pilot Grants Call — Lexogen RNA-Seq Lunch & Learn this Thursday, March 15th — Dovetail Genomics: Building the Best Genomes on Earth , April 18th

    March 13, 2018
    Dear DNA Tech Core users, the March news is: 1) a Pilot and Feasibility Project Grants Call by the Office of Research    (apply for single-cell gene expression projects) 2) the Lexogen RNA-Seq Lunch & Learn Seminar — this Thursday, March 15th — 12:30pm 3) Dovetail Genomics and the Genome Center – Building the Best Genomes on Earth — April 18th  — 1pm ******************************************************* 1) Pilot and Feasibility Project Grants Call  The Office of Research has issued a program supporting pilot and feasibility ...
  • Pilot and Feasibility Project Grants Call

    March 13, 2018
    Update: Please note that single-cell pilot and feasibility projects should be discussed with the participating cores before the application.  Our single-cell expert Diana Burkart-Waco, PhD, (dburkart@ucdavis.edu) will be available for pilot grant project related discussions every day from 3 pm to 5 pm from Thursday, March 14th to Thursday, March 22nd. To include the other cores please contact Matt Settles ...
  • January News: Batch-Tag-Seq – Gene Expression Profiling

    January 19, 2018
    Dear DNA Technologies Core Users, We are happy to announce a new service for the new year: Batch-Tag-Seq Gene Expression Profiling.  This service is designed to simplify both the planning and the analysis of gene expression profiling studies. Batch-Tag-Seq is offered as packages that include both, library preps and sequencing, as well as optionally also data-analysis. Batch-Tag-Seq combines the simplicity ...
  • Holiday Schedule

    November 27, 2017
    Except the official university holidays, the DNA Technologies Core will be open throughout the holiday season. The university holidays are December 22nd 2017, December 25th and 29th, as well as January 1st, 2018. However, please do not ship any samples with courier services for arrival in the time frame of December 22nd to January 1st. The Genome Center doors will ...
  • Genotyping and Genotyping-By-Sequencing Meeting, UC Davis Genome Center, December 5th — Genotyping Workflows: From Sequencing and Arrays to Data Analysis

    November 21, 2017
    Dear DNA Technologies Core User,   We are happy to announce the Genotyping and Genotyping-By-Sequencing Meeting in the UC Davis Genome Center for December 5th.  The talks will introduce the basic concepts as well as the latest technologies.   Lunch will be provided. Please see the announcement and the registration link below.   Please also note the info for the Bay Area Illumina User ...
  • Single-Cell Expression Profiling News

    September 21, 2017
    The 10X Genomics Single Cell system is the single-cell expression profiling platform enabling the analysis of large cell numbers at the highest capture efficiency (of up to 65%). The technology allows for high-throughput single cell transcriptomics of many different cell types.  A new protocol now also allows  single-nuclei expression profiling. This progress makes the platform now applicable also to brain tissue. The flexible ...
  • 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 ...