The Genomics Core provides state-of-the-art genomic and sequencing services to support basic and translational medical research for academic institutions and industry sectors. We strive to enable access to cost-effective, customized genomic analyses, as a functional extension of your lab.

The core closely collaborates with other Upward Research Labs core facilities, UC San Francisco Center for Advanced Technology, UC San Francisco Core Immunology Lab, and 10x Genomics. Our approach of providing consultation prior to experiment design as well as incorporating the latest techniques, makes our services a crucial resource for all researchers.

Contact

Horng-Ru Lin, PhD
Core Director
Email

 

Services Provided

  • 10x Genomics Chromium single cell/nucleus solutions: 3’/5’ Gene Expression, V(D)J Profiling, ATAC and Multiome (ATAC + Gene Expression)
  • Visium spatial transcriptomics for FFPE and fresh-frozen tissues
  • Customized NGS library preparation: DNA/RNA-seq, SMART-seq, Amplicon seq, PacBio SMRT seq, CRISPR-based single-cell screens, etc.
  • Sequencing on the Illumina platforms at the Upward Research Labs Genomics Core and UC San Francisco CAT
  • Sample preparation and QC: nucleic acid extraction, DNA/chromatin shearing, Bioanalyzer analysis, nucleic acid quantitation by Qubit and qPCR
  • Bioanalyzer, Covaris S2, Qubit and Nanodrop available for use by researchers
  • Consultations on genomics, epigenomics, and transcriptomics projects

Core Members

Mylinh Bernardi
Research Scientist

Horng-Ru Lin
Core Director

Felicia Miller
Research Technologist II

Capabilities

We are committed to developing a team of genomic professionals with diverse expertise to provide consultation and customized experimentation, implement emerging technologies, and deliver high quality data.

 

Consultation: We provide consultations on experiment design, sample preparation, experimentation, and data interpretation. We involve 10X Genomics and the Bioinformatics Core in project discussions if necessary.

10x Genomics Single Cell Solutions: We provide assays to profile gene expression and open chromatin regions at the single cell level. Our services include cell/nucleus partitioning through library construction to sequencing with all necessary QC checks.

 
 

Visium Spatial Transcriptomics: Spatial transcriptomics is a next-generation molecular profiling solution that allows the researcher to gain a holistic understanding of gene expression in the tissue microenvironment. Visium projects are processed as a joint collaboration between the Histology and Light Microscopy Core and Genomics Core.

Library Construction and Sequencing: Our core is experienced in constructing libraries from a diverse set of biological systems using varied methods. We offer customized library preparation based on your project goals. Sequencing on the Illumina platforms is carried out At Upward Research Labs and UCSF CAT.

 

FAQs

How Do I Submit Samples to Your Core?

To submit samples, register and submit a request in our online system, iLab. Once we receive and approve your request, we will contact you to coordinate sample drop off.

What Are Your Sample Submission Requirements?

You can find our sample submission requirements in iLab.

What Is Your Turnaround Time?

Turnaround times may vary, depending on the queue at the time of submission but this is our general timeline.  

Service Turnaround Time
RNA extraction, Bioanalyzer, Quantitation 1 Week
Library Preparation 2–3 Weeks
Sequencing (NextSeq and iSeq) 1 Week

Note: For NovaSeq sequencing, the turnaround time will vary depending on the queue at UCSF CAT.

How Do I Acknowledge the Core in My Publications?

In publications, we ask that you include an acknowledgment to the Upward Research Labs Genomics Core, e.g., We thank [NAME] of the Upward Research Labs Genomics Core for their assistance with [ASSAY/PROJECT].

In addition, send us an email to let let us know when your Upward Research Labs-supported work is published.