Genomics and Spatial Transcriptomics - Sanford Burnham Prebys

Genomics and Spatial Transcriptomics

image of cells and dna

Overview

The Sanford Burnham Prebys Genomics and Spatial Transcriptomics Core Facility offers a comprehensive range of genomics services, including:

  • Full-service library preparation – Utilizing an automated liquid handler for fast turnaround times and minimal sample variation.
  • RNA and DNA quality assessment – Precise sizing and quantification using the Qubit Instrument and Agilent TapeStation System.
  • Next-Generation Sequencing (NGS) – Cost-effective and high-accuracy sequencing with the Element Biosciences AVITI24 system.
  • Single-cell/nuclei library preparation – Detailed cellular analysis with the 10X Genomics Chromium X and Illumina PIPseq systems.
  • Spatial transcriptomics analysis – High-resolution spatial gene expression mapping with the 10x Genomics CytAssist system and Nanostring GeoMx Digital Spatial Profiler.
  • Cytoprofiling – Multiomic cytoprolfiling with the AVITI24 platform from Element Biosciences.

To complement our technical services, we offer scientific advising to assist with experimental design and data analysis. Our close collaboration with the Bioinformatics Core ensures comprehensive support for data interpretation and meaningful insights.

For all inquiries, please contact core director Rebecca Porritt.

Services

Next-Generation Sequencing (NGS)

We offer full-service library preparation and sequencing on the Element Biosciences AVITI platform, which provides industry-leading accuracy at competitive pricing. With dual independent flow cells and a 1B read capacity, the AVITI enables high-throughput sequencing for RNA and DNA libraries.

Flow cell options:

  • 2×75bp (500M and 1B reads)
  • 2×150bp (250M, 500M, and 1B reads)
  • 2×300bp (100M and 300M reads)

NGS Library Preparation

We provide quality control (QC) and library preparation for various sequencing applications:

  • RNA Sequencing: Poly-A RNA-seq and Whole Transcriptome RNA-seq (ribo-depleted)
  • Genomic Sequencing: Whole Genome Sequencing, Whole Exome Sequencing
  • Epigenomics: ChIP-Seq, CUT&TAG
  • Indexing & Molecular Barcoding

Our epMotion 5075 liquid handling system supports high-throughput library preparation, processing up to 96 samples per batch with minimal handling variation.

Single-Cell Library Preparation

We provide single-cell library preparation from user-supplied single-cell or single-nuclei suspensions. Our available platforms include:

  • 10X Genomics Chromium X – A highly versatile system supporting:
    • Single-cell RNA-seq
    • Single-cell ATAC-seq
    • Single-cell multiomics (RNA-seq + ATAC-seq)
    • Single-cell immune profiling
    • Feature barcoding (CITE-seq, Cell Multiplexing)
    • Targeted library preparation
  • Illumina PIP-seq System – A cost-effective platform optimized for 3′ single-cell RNA sequencing (scRNA-seq).

Spatial Transcriptomics

We offer three spatial transcriptomics technologies:

  • AVITI24 Teton Cytoprofiling
    • Multiomic cytoprolfiling including Cell Paint (morphology), RNA and protein.
    • Direct In Sample Sequencing (DISS).
    • Subcellular resolution.
  • 10X Genomics Visium HD
    • Provides 2µm-resolution whole-transcriptome spatial analysis.
    • Compatible with FFPE and FF tissues, processed via the CytAssist Instrument to transfer probes to a barcoded capture slide.
    • Enables precise spatial transcript expression mapping.
  • GeoMx Digital Spatial Profiler (NanoString)
    • Enables whole-transcriptome RNA or multiplex protein analysis in FFPE and fresh-frozen tissue.
    • Regions of interest (ROIs) are defined using antibody-based tissue staining.
    • High-resolution NGS-based transcriptomic analysis with spatial context.

DNA and RNA Quality Assessment

We provide quality assessment using:

  • Qubit Fluorometer (ThermoFisher) – Highly accurate DNA/RNA/protein quantification.
  • Agilent TapeStation 4200 – Provides sizing, quantification, and integrity assessment for DNA and RNA.
  • NanoDrop Spectrophotometer – Measures nucleic acid concentration with microvolume capabilities.

Cell Line Authentication

We offer STR-based human cell line authentication using the GenePrint 10 (Promega) system.

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

  • Element Biosciences AVITI24 Sequencer – Cost-effective and high-accuracy sequencing.
  • Eppendorf epMotion 5075 Liquid Handler – Automated, high-throughput library preparation.

Single-Cell Library Preparation

  • 10X Genomics Chromium X – Single-cell transcriptomics and ATAC.
  • Illumina PIP-seq – Cost-effective 3′ scRNA-seq with flexible scaling.

Spatial Transcriptomics

  • AVITI24 Teton Cytoprofiling – High resolution and flexible multiomic cell profiling.
  • 10X Genomics CytAssist for Visium HD – High-resolution whole transcriptome mapping.
  • NanoString GeoMx Digital Spatial Profiler – Whole transcriptome & protein spatial profiling.

Common-Use Instruments

  • qPCR Systems – Roche LC480 & LC96, ABI 7900HT, Stratagene Mx3000p.
  • Plate Reader – ThermoFisher Varioskan™ LUX for absorbance, fluorescence, luminescence, and more.

Price List

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

Leadership

Peter D. Adams, PhD
Scientific Director

Rebecca Porritt, PhD
Leader, Spatial Omics
rporritt@sbpdiscovery.org

Contact

Rebecca Porritt, PhD
(858) 646-3100 ext. 5130
Email Rebecca Porritt

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

Contact the Facility