Expression Analysis Core

expression_analysis_core_bannerThe 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 ultra high throughput sequencing and Illumina expression arrays. The PacBio Iso-Seq protocol enables full-length transcript sequencing and thus the discovery new gene isoforms.  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 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
BeadXpress Genotyping
Fluidigm EP1 Genotyping
Next-Gen Sequencing (Illumina and PacBio)
Next-Gen Library Prep (RNA-Seq, miRNA, short RNA, lncRNA, total RNA, genomic)
DNA\RNA Quantification & Library QC
Single Cell Genomics
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



  • 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 . 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.