Genomics and Spatial Transcriptomics
Overview
The Sanford Burnham Prebys Genomics Core Facility offers full-service library preparation and Next Generation Sequencing on the Element Biosciences AVITI sequencer, 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 Element Biosciences AVITI sequencer. The AVITI produces exceptionally high-quality sequencing data, with industry leading accuracy, and highly competitive pricing. It is equipped with dual independent flow cells, each with 1B read capacity, enabling high throughput sequencing for RNA and DNA libraries. Bulk RNA and DNA libraries made within the core incorporate Element Biosciences Elevate adaptors with unique dual indexes enabling a streamlined library preparation and sequencing workflow. The AVITI is also compatible with Illumina sequencing libraries through a simple conversion step (included with sequencing services), and thus supports a wide range of applications.
Flow cell options:
- 2x75bp (500M and 1B reads)
- 2x150bp (250M, 500M and 1B reads)
- 2x300bp (100M and 300M)
NGS Library Preparation
We provide QC and library preparation for a range of 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 Fluent Biosciences PIP-seq system for 3’scRNA-seq.
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.
Cell Line Authentication
We provide STR-based human cell line authentication. The GenePrint 10 System from Promega is used to perform short tandem repeat (STR) analysis on genomic DNA submitted to the core. Samples can be submitted as purified genomic DNA, or cells can be spotted directly on FTA cards in media or trypsin (FTA cards are available in the core).
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 AVITI sequencer
The AVITI produces exceptionally high-quality sequencing data, with industry leading accuracy. It is equipped with dual independent flow cells, each with 1B read capacity, enabling high throughput sequencing for RNA and DNA libraries. Bulk RNA and DNA libraries made within the core incorporate Element Biosciences Elevate adaptors with unique dual indexes, enabling a streamlined library preparation and sequencing workflow. The AVITI is also compatible with Illumina sequencing libraries through a simple conversion step (included with sequencing services), and thus supports a wide range of applications.
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.
Fluent Biosciences PIP-seq equipment
Fluent Biosciences PIP-seq is a highly flexible and cost-effective platform that uses vortexing to partition single cells or nuclei with RNA capture beads for 3’scRNAseq. PIP-seq kits come in a range of sizes from 2,000 – 100,000 cells per sample.
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.
Curio Biosciences, Curio seeker
Curio Seeker is a high resolution, whole transcriptome spatial analysis technology. It is compatible with fresh frozen tissues, which are sectioned onto a tile composed of 10uM beads with barcoded mRNA capture probes. Through sequencing of barcodes and mRNA, transcript expression can be spatially resolved. Tile sizes available include 3mm x 3mm and 1cm x 1cm.
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.
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.