Genomics and Spatial Transcriptomics

Providing state-of-the-art equipment, expertise, and next-generation sequencing services.

DNA Analysis Researcher Pouring Liquid

Overview

The Sanford Burnham Prebys Genomics Core Facility offers full-service library preparation and Next Generation Sequencing on the Illumina platform, single cell library preparation using the 10X Genomics Chromium X system, multiplex gene expression analysis with the NanoString nCounter System, and assessment of DNA and RNA quality.

We are now also heavily focused on Spatial Transcriptomics, providing analysis on the GeoMx Digital Spatial Profiler and the CosMx Spatial Molecular Imager from NanoString. 

We also provide scientific advising for experimental design and analysis as well as Bioinformatics analysis performed in collaboration with the Bioinformatics Core.

For all inquiries, please contact core director Rebecca Porritt

Services

Next generation sequencing

The core provides full-service library preparation and sequencing on the Illumina NextSeq 500 sequencer. The NextSeq 500 can sequence up to 400M reads and supports single, paired-end (up to 150 bp) and indexed sequencing. This is ideal for RNA-seq, targeted sequencing and small genome sequencing.
 

NGS library preparation

We provide QC and library preparation for a range of Illumina sequencing applications:

  • Poly-A RNA-seq, Whole transcriptome RNA-seq, Low-input RNA-seq
  • Targeted (hybridization capture and amplicon sequencing)
  • Whole Genome Sequencing, Whole Exome Sequencing
  • ChIP-Seq
  • Indexing, Molecular Barcoding
     

Single cell library preparation

The genomics core provides single cell library preparation from user provided single-cell or single-nuclei suspensions. We have two systems for single cell library preparation. These include the new 10x Genomics Chromium X system which supports a wide range of applications (see below) and the BioRad ddSeq for smaller studies.

10x Genomics Chromium X supports:

  • Single-cell RNA-seq
  • Single-cell ATAC-seq
  • Single-cell multiomics (RNA-seq and ATAC-seq)
  • Single-cell immune profiling
  • Feature barcoding (such as CITE-seq and Cell Multiplexing)
  • Targeted library preparation
     

Multiplex gene expression analysis

We provide the NanoString nCounter Analysis System for multiplex profiling of mRNA, microRNA, non-coding RNA or DNA isolated from a range of cells and tissues including fresh, frozen and FFPE samples. The system can count hundreds of sequences in a single reaction, allowing for fast, high-plex analysis of samples. This is ideal for a more targeted approach to gene expression analysis, such as biomarker validation or analysis of specific pathways.
 

DNA and RNA quality assessment

We provide three instruments for assessment of DNA and RNA concentration and quality including the TapeStation (Agilent), BioAnalyzer (Agilent) and Qubit (ThermoFisher).
The TapeStation will be used for QC for all NGS library preparations to measure concentration and fragment size.
 

Spatial Transcriptomics

We offer two spatial transcriptomic technologies from NanoString; the GeoMx Digital Spatial Profiler and the CosMx Spatial Molecular Imager.

The GeoMx Digital Spatial Profiler is used to spatially resolves RNA (whole transcriptome) or proteins (up to 96) within multiple regions of interest on FFPE or FF tissue sections. A region of interest (ROI) can be defined by first staining the tissue sections with antibodies that identify various tissue compartments or cell types of interest. This allows in-depth NGS-based analysis of transcriptomic profiles in specific cell populations with morphological and spatial context.

The CosMx Molecular Imager allows for true single cell transcriptomics using in-situ high-plex technology. FFPE or FF tissue sections can be analyzed for RNA (up to 1000) or protein (up to 64) expression using unique barcoding and imaging technology. This allows for analysis of all cell types across whole tissue sections.
 

Training

We offer instrumentation training for personnel who want to reserve, and use select instruments on their own.

Equipment & Resources

NGS library preparation and sequencing

Illumina NextSeq 500 
The NextSeq supports a wide range of sequencing applications. The flexible, scalable system offers tunable read lengths and output options to support research needs. It can sequence 20 RNA-seq, or ChIP-seq libraries per day and supports Whole-Genome Sequencing and Exome Sequencing.

Eppendorf epMotion 7075 Liquid handling system
The epMotion 7075 is used for high throughput production of RNA and DNA libraries for sequencing on the NextSeq 500.
 

Single cell library preparation

10X Genomics Chromium X
A single cell profiling system that encapsulates single cells or nuclei into GEMs for unique barcoding. The chromium X is compatible with all 10x Genomics single cell assays. It allows for large-scale studies with high-throughput single cell gene expression and immune profiling. The high-throughput chips can process up to 20,000 cells per channel.

Bio-Rad ddSeq Single-Cell Isolator
The ddSeq is an alternative single library preparation system well suited for pilot studies with less than 1000 cells per sample.
 

Spatial Transcriptomics

NanoString GeoMx Digital Spatial Profiler 
The GeoMx allows whole tissue sections (fresh frozen or FFPE) to be imaged and stained for RNA or protein. Researchers can then select specific tissue regions or cell types of interest for profiling. The high-plex system can support whole transcriptome analysis for in depth transcriptomic profiling of specific cell populations with morphological and spatial context.

NanoString CosMx Spatial Molecular Imager
The CosMx is a high-plex in situ analysis platform allowing quantification and visualization of up to 1000 RNA or 64 protein analytes than can be resolved down to the subcellular level, allowing for true single cell spatial omics. This system is compatible with fresh frozen and FFPE slide-mounted tissue sections.
 

DNA and RNA assessment

Agilent TapeStation 4200
The TapeStation system provides sizing, quantitation and quality control of DNA and RNA. It is primarily used for assessing integrity of RNA samples for NGS workflows.

Agilent BioAnalyzer
The BioAnalyzer is a chip-based system that provides sizing, quantitation and quality control of DNA and RNA.

Qubit Fluorometer
The Qubit gives an extremely accurate measurement of small amounts of DNA, RNA or protein.

NanoDrop Spectrophotometer
A microvolume (1µl) spectrophotometer to measure nucleic acid concentration.
 

Common-use instruments in the Core

qPCR
  • Roche LC480 real time QPCR instrument (interchangeable 96 or 384 well)
  • Roche LC96 real time QPCR instrument
  • Stratagene Mx3000p real-time QPCR instrument (96 well)
  • ABI 7900HT real time QPCR (interchangeable 96 or 384 wells)
     
Plate Reader

ThermoFisher Scientific Varioskan™ LUX multimode microplate reader
Supports a range of measurements including Absorbance, Fluorescence Intensity (top or bottom), Luminescence (with 2 dispensers), AlphaScreen, and Time-Resolved Fluorescence.

Price List

For a complete list of services, please call (858) 646-100 ext. 5130 or email us.

Leadership

Leader, Spacial Omics

Contact

Rebecca Porritt, Ph.D.
(858) 646-3100 ext. 3714
Email Rebecca Porritt

Please call (858) 646-3100 ext. 5130 or use the button below to send us an email.

Contact the Facility