Genomics and Sequencing



Stein Clinical Research Building
UC San Diego
9500 Gilman Drive, MC 0679
La Jolla, CA 92093-0679

Phone: 858-552-8585, ext. 2585



The Genomics and Sequencing Core services include:

1. Nucleic acid isolation, quantification and quality control

2. Relative and absolute quantification of gene expression using real-time quantitative qPCR technology (TaqMan and SYBRGreen) and droplet digital PCR (ddPCR).

A. mRNA and long non-coding RNA
B. microRNA
C. Viral RNA (HIV and other viruses)

3. Next generation sequencing

A. MiSeq and Ion S5/Ion Chef system for multiple assays: targeted resequencing, bacterial sequencing, general purpose (coverage up to 16,000 reads)
B. HIV quantitative integration assay
C. Single cell sequencing sample and library preparation (10X Genomics platform)

4. Bioinformatics

A. Pipeline for processing raw RNA-Seq data using Shell script in Linux environment
B. Analysis of RNA-Seq data in Bioconductor R
C. Downstream analysis of the genes of interest (pathway and GO term enrichment)
D. Analysis of single cell RNA-Seq data in development
E. HIV integration site analysis pipeline

At a Glance