The 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.
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
Fluidigm EP1 Genotyping
|Next-Gen Sequencing (Illumina and PacBio)
Next-Gen Library Prep
DNA Quantification/Library QC
Single Cell Genomics
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
- January 19, 2018Dear 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 ...
- November 27, 2017Except 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 AnalysisNovember 21, 2017Dear 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 ...
- September 21, 2017The 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 ...
- May 12, 2017August 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 ...
- April 19, 2017Illumina 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 ...
- April 11, 2017A “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 selectionApril 6, 2017New 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 ...
- March 9, 2017PacBio 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 ...
- December 15, 2016We 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.