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 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
|Illumina Sequencing HiSeq 3000, HiSeq 2500 & MiSeq
PacBio Sequencing PacBio RSII
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 (RNA-Seq, miRNA, short RNA, lncRNA, total RNA, genomic)
DNA\RNA 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 BluePippin
Automated Library Prep: Caliper Sciclone G3, IntegenX Apollo 324, Fluidigm Access Array
- 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.
Seminar: Simultaneous “multi-omic” measurement of gene fusions, mRNA, & proteins at 800-plex using single-molecule optical barcodesNovember 11, 2016Please 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 ...
- November 10, 2016Pacific 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 2017October 27, 2016February 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 ...