Shared Resource Archives - Sanford Burnham Prebys

Page Type: Shared Resource

CODEX

Overview

CODEX is a highly multiplexed spatial proteomics technology that enables simultaneous detection of dozens of protein markers within intact tissue while preserving their spatial context. By combining multiplex antibody imaging with high-resolution microscopy, CODEX allows researchers to characterize tissue architecture, cellular composition, and cell-to-cell interactions at single-cell resolution.

Compared with conventional immunofluorescence and lower-plex imaging approaches, CODEX enables the analysis of many biomarkers within the same tissue section, providing a more comprehensive view of complex tissue microenvironments while preserving spatial information.

The CODEX Core provides end-to-end spatial proteomics services, including experimental design, antibody panel development and conjugation, multiplex imaging, and comprehensive downstream data analysis. Trained users may also access selected instruments for independent use, including self-operated imaging on the Keyence microscope and cryostat sectioning following completion of the required training.

Investigators are encouraged to consult with the Core early in the experimental design process for guidance on tissue preparation, biomarker selection, panel optimization, and imaging strategies. Early consultation can help ensure compatibility with the CODEX workflow and maximize the quality and biological value of the resulting spatial proteomics data.

Services

From study planning to data interpretation, the CODEX Core offers comprehensive support for spatial proteomics projects. Services include:

  • Scientific consultation and project planning
  • Tissue preparation and sectioning
  • Antibody panel design and custom conjugation
  • Multiplex tissue staining
  • High-dimensional imaging using the PhenoCycler™ platform
  • Image processing, spatial analysis, and biological interpretation

Additional Services

  • Keyence microscope training
  • Self-operated Keyence microscope imaging (available to trained users)
  • Self-operated cryostat sectioning

Panels Available

We currently have established CODEX panels available for several tissues and biological systems, including:

  • Liver
  • Muscle
  • Epigenetic panel
  • Tumor tissue
  • Immune tissues
  • Brain
  • Lectin-based panels

Equipment & Resources

The CODEX Core is equipped with:

2 × PhenoCycler™ Open Systems (Quanterix)
Each instrument is integrated with a high-resolution Keyence fluorescence microscope, enabling automated cyclic imaging of multiplex antibody panels and generation of spatially resolved protein expression datasets.

2 × Keyence BZ-X810 Automated Fluorescence Microscopes
Microscope capabilities include:

  • Air objectives: 4×, 10×, 20×, and 40×
  • Optional oil immersion objective: 63× / 1.40 NA
  • Multi-channel fluorescence imaging capabilities, including:
    • Blue: DAPI, Hoechst, BFP
    • Green: GFP/YFP, FITC, Alexa Fluor™ 488
    • Red: TRITC, Cy3, Rhodamine, Alexa Fluor™ 546
    • Far-red: Cy5, APC, Alexa Fluor™ 647
    • Near-infrared: Cy7, Alexa Fluor™ 750

3 × High-Performance Image Analysis Workstations
The Core provides dedicated computational resources for processing and analyzing large-scale spatial imaging datasets. Workstations are equipped with high-performance NVIDIA GPUs (24 GB VRAM) to support image processing, cell segmentation, spatial analysis, and downstream data interpretation.

250 TB Secure Network Storage
A dedicated high-speed data infrastructure, including a 10 Gigabit Ethernet network and QNAP Network Attached Storage (NAS) systems, enables efficient transfer, management, and secure storage of large multiplex imaging datasets.

Epredia CryoStar™ NX50 Cryostat
The Core provides cryostat sectioning capabilities using an Epredia CryoStar™ NX50 cryostat equipped with Vacutome technology and adjustable chamber height, supporting high-quality tissue preparation for spatial proteomics applications.

Price List

For a complete list of services, please call (858) 646-1000 ext. 4180 or email us.

CODEX Services Internal
Subsidized 		Internal External
Non-Profit 		External
For-Profit
ConsultationFreeFreeFreeFree
Coverslip Coating (Batch of 20)$100$125$135$263
Tissue Sectioning (per hour)$100$125$135$263
H&E Staining$100$125$135$263
Multiplex Staining$730$913$968$1,920
Antibody MixVariable (see formula below)
Plate Preparation – Small Panel$150$188$203$395
Plate Preparation – Large Panel$180$225$243$473
Antibody Panel Design (per hour) $150$188$203$395
Antibody Conjugation (Each) $80$100$108$210
Imaging Service – Validation Panel $500$625$675$1,315
Imaging Service – Regular Panel Variable (see formula below)
Data Analysis (per hour) $90$113$122$237
Keyence Microscope Training (per hour) $70$88$95$184
Self-Operated Keyence Microscope Imaging (per hour) $30$38$40$80
Self-Operated Cryostat Sectioning (per hour) $80$100$108$210

Antibody Mix Cost
Estimated Cost = Antibody Total Mix Volume (µL) × $3 per µL +$150 (prep fees)

Imaging Service – Regular Panel Pricing
Estimated Cost =(Number of Tiles×$0.40)×(Number of Regions×$0.70)×(Number of Cycles×$0.50)+$150​
Note: The $150 surcharge applies only to experiments with 20 or more imaging cycles.

Leadership

Beatrice Silvestri, PhD
CODEX Core Manager
(858) 646-3135
bsilvestri@sbpdiscovery.org

Contact

Dr. Beatrice Silvestri is a neuromuscular biologist with expertise in advanced imaging technologies, spatial biology, and multiplexed tissue profiling. She received her PhD training at Sapienza University of Rome, Italy, and completed her postdoctoral training in the laboratory of Dr. Yu Xin Wang at Sanford Burnham Prebys.

Her research has focused on applying high-dimensional imaging approaches to understand complex tissue microenvironments, including immune regulation, tissue regeneration, and disease-associated changes. Dr. Silvestri has extensive experience with the Akoya CODEX/PhenoCycler platform, including the development and optimization of spatial proteomics workflows, multiplex antibody panel design and validation, tissue preparation strategies, image acquisition, and computational analysis of large-scale spatial datasets.

As Manager of the CODEX Core, Dr. Silvestri provides scientific guidance and technical support to investigators throughout all stages of their projects, from experimental design and assay development to spatial data interpretation. She works closely with researchers to develop customized solutions that enable robust and reproducible spatial profiling studies across a variety of biological applications.

Please call (858) 646-3135 or use the button below to send us an email.

Contact the Facility

Exploratory Pharmacology

scientist working in a lab

Overview

The Exploratory Pharmacology group delivers rapid, high-quality assessments of drug-like properties to support informed decision-making by medicinal chemistry teams during drug development. Leveraging deep scientific expertise and optimized workflow infrastructure, the group enhances efficiency across the drug discovery pipeline, from hit identification to candidate selection.

Tier 1 ADME
In vitro		Tier 2 ADME
In vitro		Drug-like Properties
In vivo
Kinetic SolubilityCyp P450 inhibitionAnalytical method development
Thermodynamic solubilityIn vitro hERG bindingIV/IP/PO Pharmacokinetics
Microsomal StabilityMetabolite profilingOral bioavailability
Hepatocyte StabilityPlasma Protein BindingFormulation screening
Plasma StabilityTissue free fractionTissue/CNS Distribution

Comprehensive ADME Profiling 

The bioanalytical facility performs critical drug discovery ADME (Absorption, Distribution, Metabolism, Excretion) assays, including:

  • Solubility assessments under physiologically relevant conditions
  • Metabolic stability studies in liver microsomes and hepatocytes (mouse, rat, human, minipig, dog and others on demand)
  • Plasma protein and tissue binding experiments
  • Cytochrome P450 inhibition screening
  • Metabolite profiling and identification

Advanced Bioanalytical Capabilities

The team utilizes state-of-the-art Triple Quadrupole mass spectrometry (API 6500+ QTRAP) for ultra-sensitive quantification of drug concentrations in plasma/tissue samples. This technology enables analysis of exceedingly small sample volumes (5 µL), surpassing traditional PK protocols.

Highly efficient Micro-PK Study 

A combination of saphenous, retro-orbital, and terminal bleeding techniques allows serial blood sampling (~10–15 µL per draw) from individual mice at up to 8 time points (0–24 hours post-dose). This micro-sampling approach, paired with high-sensitivity bioanalysis, generates complete PK profiles using only 3 mice per arm, minimizing animal use and reducing costs. Routinely conducted routes of administration include Intravenous (IV), Intraperitoneal (IP), Oral (PO), Subcutaneous (SC) and Topical administration routes. 
The micro-PK procedure described is highly cost-effective as it minimizes the number of animals required while generating complete pharmacokinetic (PK) profiles from each subject. By employing micro-sampling techniques, only 3 mice per PK arm are used, significantly reducing animal use compared to traditional protocols. This approach not only lowers costs but also ensures ethical compliance by minimizing the number of animals needed for research. Additionally, the procedure utilizes advanced bioanalytical infrastructure, such as Triple Quad mass spectrometry, to extract comprehensive PK profiles from exceedingly small sample volumes, maximizing efficiency and accuracy.

External Study Support

The facility also analyzes samples from in vivo PK/PD studies performed outside of Prebys Center, offering:

  • Drug level quantification via LC-MS/MS (Shimadzu UHPLC with Nexera SIL-30ACmp autosampler coupled to AB SCIEX API 6500+ QTRAP®/API 4000 systems) with a typical limits of quantification typically less than 1nM.
  • Metabolite profiling

Extended Pharmacological Services

Additional capabilities include:

  • Formulation screening for optimal bioavailability
  • Allometric scaling and human dose predictions
  • AI/ML-driven predictions for key pharmacological properties (e.g., brain penetration, CYP lability, P-gp interactions, metabolic pathways) for academic collaborators.
  • We also have access to reliable vendors who perform high quality studies including permeability, CYP induction, met-ID, genotoxicity and other assays.

By integrating cutting-edge technology with specialized expertise, the Exploratory Pharmacology group accelerates the identification of viable drug candidates while adhering to ethical and cost-effective practices.

Services

Assays

  • Stability
    Liver microsome, hepatocyte, plasma and formulation stability
  • Solubility
    Kinetic and thermodynamic solubility
  • Free fraction determination
    Plasma protein binding and brain fractionation
  • PK and bioavailability studies
    IV, IP, PO, SC, topical etc. 
  • Dose predictions
    Clearance, Brain weight and Maximum Lifespan Potential based First-in-Human predictions
  • PD and efficacy studies
    In vivo models for assessing target engagement, functional activity and assessment of drug like properties

Equipment & Resources

Sciex QTRAP 6500+

Brings about significant enhancement in our bioanalysis capabilities

  • Linearity: Triple quadrupole has one of the best range of linearity with MRM3 mode (up to 6 orders of magnitude)
  • Sensitivity: LLOQ in pg/mL to fg/ml ranges (results vary for analytes; Attograms sensitivity reported for some analytes)
  • Agility: Polarity switching (1millisecond)
  • Versatility: Mass range of m/z 5 – 2,000
  • Robustness: Multi-day consecutive injection feasible
  • Efficiency: Increased ionization efficiency and heat transfer with the new IonDrive Turbo V source
Product photo of Sciex-QTRAP-6500

Sciex API 4000

For ADME and bioanalysis

  • Linearity: Triple quadrupole has one of the best range of linearity with MRM3 mode (up to 6 orders of magnitude)
  • Sensitivity: LLOQ in ng/mL ranges (results vary for analytes; picograms sensitivity reported for some analytes)
  • Agility: Polarity switching
  • Versatility: Mass range of m/z 5 – 1,000
  • Robustness: Multi-day consecutive injection feasible
  • Efficiency: Increased ionization efficiency and heat transfer with the new IonDrive Turbo V source

Shimadzu UPLCs

Shimadzu UPLCs with advanced SIL-30 autosamplers are designed to deliver exceptional performance in bioanalytical experiments. These systems feature ultra-low carryover, rapid injection cycles, and precise sample handling, ensuring reliable and reproducible results. The needle-in-flow path design minimizes contamination by continuously flushing the sample path with the mobile phase gradient. With capabilities such as temperature-controlled sample cooling for heat-sensitive compounds, automated pretreatment functions, and dual injection modes, these autosamplers enhance throughput and precision while reducing manual intervention. Their compatibility with LC-MS/MS systems makes them ideal for high-sensitivity applications, enabling accurate quantification and profiling of analytes in complex biological matrices.

Price List

For a Price List, please call (858) 795-5164 or email us.

Medicinal Chemistry

scientist working in a lab

Overview

The Medicinal Chemistry Facility at Sanford Burnham Prebys Medical Discovery Institute provides synthetic and medicinal chemistry resources and expertise to the biomedical research community at the Institute and to external academic partners. Our team is staffed with industry-trained chemists skilled in all aspects of small-molecule synthesis and medicinal chemistry. We collaborate closely with other shared resource groups at SBP to drive projects forward from conception to clinical translation.

Services

Chemistry Consulting for Projects and Grant Applications

  • Analysis of prior art, chemical landscape, and patentability

Synthetic and Medicinal Chemistry

  • Develop structure-activity relationships (SAR), based on biological assay results, and recommend next step decisions for project progression
  • Synthesize small molecule reference compounds from milligram to multi-gram scale
  • Design and synthesize chemical libraries for hit and lead identification, as well as diversity libraries based on a structural theme
  • Prepare custom organic reagents and synthetic intermediates
  • Analog synthesis and lead optimization targeting the improvement of potency, physiochemical, and pharmacokinetic (PK) properties

Computational Chemistry and AI

  • Experience using state-of-the-art computational tools for advancing projects from target evaluation to lead optimization
  • In silico screening of large virtual libraries to identify novel probes and hits for drug discovery
  • High-performance computing cluster (Pines) supporting docking, molecular dynamics, and machine-learning workflows
  • AI tools to predict druggability, ADME/PK properties, and ligand-protein interactions

Analytical Chemistry

  • 1H,13C,19F NMR with 2D heteronuclear spectra acquisition and variable temperature capability
  • Verification of the structural identity and purity of samples
  • HPLC and LC/MS analysis
  • Triple quadrupole MS/MS analysis
  • Normal phase, chiral, and reverse phase chromatography separations on analytical and/or preparative scales.

Core Services PDF

Equipment & Resources

The Medicinal Chemistry core occupies approximately 2000 sq. ft. of laboratory space and is equipped with cutting edge synthetic and analytical equipment.

Synthesis Equipment

  • 14 6ft chemical fume hoods
  • Biotage and CEM microwave synthesizers with robotic processing
  • Parr shaker hydrogenation apparatus
  • Two Genevac evaporation systems
  • Multiple FreezeMobile 25EL lyophilization units

Analysis and Purification Equipment

  • Four Teledyne-Isco flash chromatography systems with multi-column functionality and UV detection
  • Two Teledyne-Isco ACCQprep HP150 preparative HPLC systems with UV detection
  • Two Shimadzu preparative HPLC systems with UV detection
  • Thermo-Fisher Ultimate 3000 preparative HPLC with UV detection
  • Waters Acquity LC/MS with ESI ionization source and PDA detector
  • Shimadzu LC/MS 2020 with ESI ionization source and PDA detector
  • Agilent Pro iQ LC/MS with ESI ionization source, PDA detector, and 364-well plate capability
  • Applied Biosystems API 3000 for LC/MS-MS studies
  • 400 MHz JEOL NMR spectrometer with autosampler

Price List

For a Price List, please call (858) 646-3100 ext. 5320 or email us.

Leadership

Michael Jackson, PhD
Vice President, Drug Discovery & Development

Steven Olson, PhD
Facility Director
solson@sbpdiscovery.org

Contact

Please call (858) 646-3100 ext. 5320 or use the button below to send us an email.

Contact the Facility

High-Throughput Screening

close-up photo of lab equipment

Overview

The Screening & Chemical Libraries (S&CL) facility — home of the Center’s High-Throughput Screening (HTS) capabilities — provides the instrumentation, compound libraries, and expertise needed to screen chemical libraries against biological targets. The facility offers diverse screening instrumentation, curated compound collections, and deep expertise in high-throughput screening and laboratory automation, supporting collaborative, user-driven, and facility-driven screening projects. S&CL works closely with assay-development and high-content/imaging colleagues to select and implement the most suitable biochemical or cellular assay for each project, spanning a wide range of plate-reader and imaging formats.

S&CL is part of the Therapeutics Discovery Shared Resource (TDSR), an integrated, end-to-end drug-discovery resource that spans target validation through preclinical lead optimization. As the hit-identification engine of TDSR, S&CL connects seamlessly with structural biology (cryo-EM), medicinal and computational chemistry, and predictive pharmacology (ADME/PK) teams — giving investigators a continuous path from a biological hypothesis to an optimized, preclinically validated lead compound.

The Center maintains collaborations with a select group of pharma and biotech organizations, as well as several clinical hospitals, to develop small-molecule therapeutics, and continues to seek additional partnerships of mutual benefit. These partnerships typically involve a portfolio of projects that the Center drives — in collaboration with the partner — through the early stages of drug discovery (assay development through lead optimization to in vivo proof-of-concept). Engagements often begin as a pilot project that evolves into a broader collaboration or “shared pipeline.”

The Screening & Chemical Libraries facility within the Therapeutics Discovery Shared Resource, which integrates screening, structural biology, medicinal/computational chemistry, and predictive pharmacology into a single end-to-end drug-discovery pipeline.

Services

  • Screening of small-molecule compound libraries in 384- or 1536-well formats using a range of detection technologies (absorbance, fluorescence, luminescence, fluorescence polarization [FP], TR-FRET, and AlphaScreen).
  • Consultation on high-throughput screening strategy, assay design, and detection-technology selection.
  • Conversion of cell-based and biochemical assays into high-throughput / automation-compatible formats.
  • Preparation and handling of compound libraries for high-throughput screening, including pre-spotted plates for rapid pilot screens (members pay only a nominal distribution cost).
  • Rapid hit validation and expansion, including access to on-demand virtual libraries for analog follow-up.
  • Screening data analysis and support for HTS hit follow-up studies (e.g., dose–response confirmation and cherry-picking).
  • Assistance with, and hands-on training on, automated instrumentation — including the three Access Workstations, the EnVision and PHERAstar plate readers, and the Phenix imaging platform.

Opportunity

Therapeutics Discovery Shared Resource (TDSR) facility is open to multiple engagement models tailored to partner needs.

Organization Types

  • Academic investigators needing US-based drug discovery support for NIH grants with foreign component restrictions
  • Biotech companies seeking integrated medicinal chemistry and pharmacology without building in-house capabilities
  • Investigators seeking hit identification through ultra-high-throughput screening of large diverse compound libraries
  • Non-profit disease foundations looking to de-risk early-stage therapeutic programs
  • Government agencies and research consortia needing contract research with scientific depth

Beyond Fee-for-Service
Scientifically guided project support where TDSR scientists contribute expertise throughout the drug discovery process, providing strategic value beyond data generation. Ideal for investigators who need a collaborative partner, not just a service provider.

Strategic Partnership
Longer-term, multidisciplinary collaborations to advance translational research programs. TDSR supports grant applications (including multi-PI and U01/U19 mechanisms), co-develops project strategy, and commits resources to shared milestones. This model is well-suited for organizations seeking a sustained drug discovery partner.

Contract Research
Defined-scope projects with specific deliverables — assay development, compound synthesis, PK studies, or hit-to-lead campaigns with clear milestones and timelines.

Sponsored Research
Industry-funded research programs conducted within the SBP academic environment, leveraging the Institute’s biological expertise alongside CTD chemistry and pharmacology.

TDSR also welcomes pilot projects as a way for new partners to evaluate capabilities before committing to larger programs.

Certain resources, including compound collections and software licenses, were acquired under third-party agreements that specify non-profit or collaborative use. We can advise on options to accommodate fee-for-service projects with for-profit entities, please contact us for details.

Compound Libraries & Collections

The facility maintains a diverse, continually curated compound collection for exploratory and translational cancer research. Specialty collections are assembled in consultation with Center faculty and combine vendor libraries with non-commercial, literature-described compounds synthesized by our medicinal chemists.

  • More than 310,000 diverse, drug-like compounds procured from ChemBridge and Enamine.
  • Over 20,000 bioactive compounds organized into specialty sub-libraries, including kinase inhibitor, epigenetics, protease inhibitor, structure–activity relationship (SAR), fragment, re-purposing, and FDA-approved collections.
  • Focused collections — Epigenetics, Kinase Inhibitors, Protease Inhibitors, and Mechanism-of-Action — curated from faculty recommendations.
  • On-demand access to virtual libraries of ~4.4 trillion make-on-demand compounds (including the Enamine REAL / xREAL database) for rapid hit validation and analog expansion.
compound libraries and screen modalities

Left: composition of the facility’s physical compound libraries and specialty collections. Right: distribution of assay/detection modalities across screens performed over the last five years.

Detection & Assay Modalities

The facility supports a broad range of biochemical and cell-based readouts in 384- and 1536-well formats:

  • Absorbance
  • Fluorescence intensity
  • Fluorescence polarization (FP)
  • Luminescence (including glow luminescence)
  • FRET / TR-FRET
  • AlphaScreen
  • Phenotypic / high-content (imaging) readouts in collaboration with HCS core
  • NMR-based screening in collaboration with Med. Chem. core

Equipment & Resources

  • Automated Liquid Handling & Compound Dispensing
    • Three Access™ Laboratory Workstations (Labcyte/Beckman), built around two Echo 655s and an Echo 555 acoustic liquid handler with a precision robotic arm, random-access plate racks, a de-lid station, a low-volume bulk dispenser, a microplate centrifuge, a plate peeler, and an Agilent PlateLoc sealer with Argon gas purge, controlled by Labcyte TEMPO automation software. The three systems are configured for distinct workflows — Biochemical Screening, Cellular Screening, and SAR Support; the Cellular Screening workstation additionally integrates a Thermo Scientific Cytomat automated incubator for fully automated cell-based HTS. These systems enable fully automated, multi-plate, small-volume dispensing — particularly useful for dose–response testing of large compound sets and cherry-pick confirmation of primary hits.
    • Plate-processing workstation (Agilent) — a Bravo automated liquid handler with a BenchCel 4x plate handler (four stacker towers), an Agilent PlateLoc thermal sealer, and a Vcode barcode label print-and-apply system.
    • Two Beckman Coulter Biomek FX liquid-handling systems (one fully enclosed) with 96- and 384-well multichannel heads and Span-8 arms.
    • Two TTP Labtech (SPT Labtech) Mosquito nanoliter liquid handlers for low-volume, positive-displacement transfer (assay miniaturization, qPCR setup, and dose–response preparation).
    • Two Certus FLEX digital dispensers (Fritz Gyger micro-valve technology) for contactless, nanoliter-to-microliter dispensing of up to eight fluids.
    • Three INTEGRA WELLJET reagent dispensers for fast, precise bulk plate filling (0.5 µl–10 ml, 6- to 1536-well formats).
    • Multiple Thermo Scientific Multidrop Combi / Multidrop DW bulk reagent dispensers.
  • Detection & Kinetics Instruments
    • Revvity EnVision Nexus multimode reader with stackers and Alpha capability for walk-away, high-throughput detection housed in a dedicated, environmentally controlled ‘green-room’ suite
    • Hamamatsu FDSS/µCELL kinetic plate imager — a high-speed, whole-plate fluorescence and luminescence imager with simultaneous dispensing to all wells (e.g., for GPCR, calcium-flux, ion-channel, glow-luminescence, and enzyme-kinetics assays).
  • Stand-alone Instruments
    • Two Labcyte Echo 555 acoustic liquid handlers
    • BMG LABTECH PHERAstar FSX multimode plate reader (stand-alone, with plate stacker) –An additional BMG LABTECH PHERAstar FSX equipped with injectors and lasers
    • BioTek plate washers — two EL406 washer dispensers and an ELx405 Select CW washer
    • BlueCatBio BlueWasher centrifugal plate washer for gentle, near-zero-residual-volume washing of cellular and bead-based assays (96- to 1536-well).
    • Agilent PlateLoc thermal plate sealers and plate label print-and-apply systems.
    • Six Applied Biosystems ViiA 7 real-time PCR systems and four Eppendorf Mastercycler X50 thermal cyclers (shared with Assay Development).
  • Compound Management & Sample Handling
    • Sensitive Mettler Toledo analytical and micro balances in draft enclosures for precise compound weighing.
    • 2D-barcoded tube scanning and tracking: LVL technologies whole-rack 2D-barcode scanners and a BioMicroLab SampleScan Mini, using LVL SAFE -barcoded storage tubes.
    • Automated LVL tube decapping/recapping: single-row and full-plate (96-format) decappers for 2D-barcoded compound tubes.
    • Tube and plate labeling for compound tubes and plates: Brady thermal label printers and an LVL plate sealer.

Price List

For a Price List, please call (858) 795-5164 or email us.

Leadership

Raghuveer Ramachandra, PhD
Director, Automation and Drug Discovery Services
erramachandra@sbpdiscovery.org

Contact

Please call (858) 795-5164 or use the button below to send us an email.

Contact the Facility

High Content Screening

Close-up shot of a scientists hands working with lab equipment

Overview

The High-Content Screening (HCS) core facility of the Conrad Prebys Center for Chemical Genomics is part of the Sanford Burnham Prebys screening center. As part of the Prebys Center, the HCS resource has access to the HTS plate and liquid handling infrastructure of the screening center as well as the screening center’s cell culture facility. For details on the other core facilities of the Prebys Center, please refer to the “Related Resources” below.

The HCS core facility provides assay development, screening, and data analysis/mining expertise and services for high content screens, where the readout is based on images obtained using high-throughput microscopy systems. For assay development and screening of non-imaging assays refer to Assay Development and High-Throughput Screening. The HCS team has expertise in all areas of high content image-based screens including sample preparation, image acquisition, image analysis, image data management, and algorithm development.

The HCS core has experience conducting phenotypic assays, ranging from functional assays, such as inhibition of phagocytosis and quantification of cytoskeletal changes, to transcriptional reporter modulation, such as activation of insulin promoter activity. HCS projects range from screening of several hundred chemical compounds to libraries of over 300,000 compounds. Additionally, the Prebys Center screening center is co-located with the Sanford Burnham Prebys Functional Genomics (FGC) core, fostering collaboration between the HCS and FGC resources for RNAi screening projects.

Services

The HCS core facility’s experienced staff is available to help investigators design and execute image-based assays by providing the following services:

  • Conceptualization and design of image-based assays for medium- and high-throughput screening.
    • For small scale screens:
      • Training/use of HCS instruments
      • Training/use of analysis software
      • Performing selection, development, and/or validation of image analysis methods and/or assay read-outs
    • For large scale screens:
      • Optimizing assay biology
      • Developing algorithms and read-outs
      • Performing assay miniaturization/validation
      • Screening in collaboration with HTS or Functional Genomics facilities
  • Aid in image data management, HC data analysis and visualization
     

HCS Project Examples

Image-based high content assays are usually employed when an assay utilizes multiplexed fluorescent labels, investigates sub cellular localization or spatial distribution of fluorescence. The technique can also be used when evaluating morphological changes of cells or cellular structures such as shape or size, quantifying co-localization of multiple labels, or monitoring the response of a sub-population of cells. Because of the high content nature of image-based assays, the multi-parametric assay read-outs can provide additional biological or disease relevant information. Some examples of medium and high throughput screening campaigns utilizing image-based high content assays are provided in the table below.

Equipment & Resources

Liquid Handling

Robotic liquid and plate handling equipment and resources are used in common by all groups within the Prebys Center and are described in detail under High Throughput Screening. For information on available screening libraries, refer to Compound Management for chemical libraries and Functional Genomics for RNAi libraries.

HCS imaging systems

The HCS core facility contains state-of-the-art automated high-throughput microscopy instruments. Depending on the instrument, autofocusing is either image-based (IC200, Eidaq100) or laser-based (IN Cell 1000, Opera QEHS, Celigo). These instruments can be used with different objectives ranging from 4x to 60x magnification and have the ability to image standard clear-bottom multi-well plates (96, 384, 1536), preferably black plates with optical quality glass or plastic bottoms with a bottom thickness of ~200um. The INCell1000 and Opera QEHS in La Jolla have automatic plate loading capabilities (>40 plates). For a summary of each HCS instrument’s capabilities refer to the table below.

HCS image analysis and image data management software

A variety of image processing, data analysis, and visualization tools are available, including InCell Investigator (GE), CytoShop (Q3DM/Beckman Coulter), CyteSeer (Vala Sciences), Acapella (PE), Matlab (The Mathworks), Photoshop (Adobe), ImageJ (NIH), CellProfiler/CellVisualizer (nonprofit open source), and Volocity 3D/time course analysis software (PE). For screen data analysis and mining, CBIS (ChemInnovation) screening database software, as well as Spotfire (Tibco), Genedata Screener, and Prism (Graphpad) data analysis software are available. With these software packages the HCS team can rapidly apply available HCS solutions and algorithms, as well as develop custom HCS solutions, algorithms and tools for the wide variety of HCS projects.

To streamline HCS processing, visualization, and data management, the HCS team implemented a local storage system (LSS) dedicated to HCS based on the Columbus image-data management system (PE). The Columbus system provides ~12TB of fast access storage at the La Jolla site and handles image and data file management for currently ongoing HCS projects. The LSSs is connected via high-speed intranet and provide scientists with web-based access to image visualization, analysis, and data visualization tools. The Columbus image-data management system provides web-based upload capabilities for Opera, INCell 1000, IC200, Eidaq100, and Celigo instruments. It is integrated with the Volocity 3D/time course visualization and analysis package, and is also directly linked to Genedata Screener software for a complete HCS image-data analysis and visualization solution.

Price List

For a Price List, please call (858) 646-3100 ext. 3329 or email us.

Leadership

Michael Jackson, PhD
Vice President, Drug Discovery & Development

Susanne Heynen-Genel, PhD
Facility Director
sheynen@sbpdiscovery.org

Contact

Please call (858) 646-3100 ext. 3329 or use the button below to send us an email.

Contact the Facility

Assay Development

chemistry assay-pub domain

Overview

The Assay Development core facility performs design, development, validation and pilot screening of biological high-throughput assays. Our dedicated staff is skilled in various screening modalities to help design and develop de-novo assays or convert low-throughput lab protocols (e.g., cuvette- or gel-based) into plate-based HTS assays. To date, the facility has developed more than 250 cell-based and biochemical assays. Approximately half of these assays advanced to HTS, and the other half are employed in assay panels supporting HTS hit validation and Structure-Activity Relationship (SAR) studies. The facility is an integral part of Conrad Prebys Center for Chemical Genomics and works closely in collaboration with other cores and teams.

The HTS Assay Development core also provides direct assistance with preparing screening-related grants, guiding through assay development stages, helping design testing funnels, and generating preliminary data.

Services

  • Consultations on suitable screening alternatives and selection of the approaches consistent with project goals
  • Implementation and optimization of previously established screening protocols
  • Design and development of HTS assays
    • Cell-based and biochemical assays in 96-, 384- and 1536-well plate formats
    • Assays based on variety of HTS detection approaches (absorbance, fluorescence, fluorescence polarization, luminescence, AlphaScreen, BRET, FRET, TR-FRET)
    • Multiplexed cell-based assays for simultaneous assessment of multiple cellular functions, e.g. multiplexed qPCR assays, or reporter gene expression and cell viability
    • End-point and kinetic assays using common and special screening equipment
    • Functional and binding assays, including Differential Scanning Fluorimetry (also called protein thermal shift) assays detecting direct small-molecule binding through stabilization of target proteins in thermal denaturation
  • Assay optimization, miniaturization and implementation
    • Optimization of common assay parameters, such as cell density, ligand and enzyme concentrations, assay media or buffer
    • Evaluation of DMSO concentration effects
    • Optimization of assay sensitivity for identification of compounds with desired MOA
    • Evaluation and optimization of assay statistics and reproducibility
  • Focused library pilot screening
    • Assessment of assay performance measures (signal-to-noise, signal-to-background, assay dynamic range, Z’-factor) and their reproducibility
    • Evaluation and optimization of HTS hit rate
    • Access to a wide selection of focused libraries, e.g. collections of known drugs, kinase inhibitors, NCI compound sets (please inquire about the full list of focused libraries)
  • Support for Structure-Activity Relationship (SAR) studies:
    • Design and implementation of SAR panels relevant to the project goals
    • Development of secondary (e.g. orthogonal, counter-screen) assays
    • SAR data analysis and interpretation
    • Mechanism of action studies: determination of compound’s Ki, competition profile and time-dependent effect
  • Assistance with the preparation of screening grants
    • Consultation on available funding mechanisms (e.g. NIH PAR-12-058 and PAR-12-059)
    • Help in development of specific aims and project plan
    • Hands-on support in generation of preliminary data
    • Expertise with diverse target classes and multiple formats utilized at the facility and its application for selecting secondary assays and designing project workflow

Equipment & Resources

Major Robotic Equipment and Resources used by Assay Development at the Conrad Prebys Center for Chemical Genomics include:

  • Hamamatsu FDSS7000 rapid-kinetics (e.g. GPCR, glow luminescence, enzyme kinetics) fluorescence and luminescence plate reader with integrated 384-well liquid handling
  • LabCyte Access Laboratory Workstation for cherry picking of screening hits and preparation of SAR compound plates
  • NEPHELOstar plate reader for detecting light scattering in 96- and 384-well plate based solutions using nephelometry approach
  • Monochromator based multimode plate readers
    • Two Molecular Devices M5 instruments
    • Molecular Devices FlexStation 3
  • Two VIIA7, 7th generation real-time PCR instruments
    • Specifically designated for development and screening of qPCR and Differential Scanning Fluorimetry (protein melt) assays
    • 384-, 96-, fast 96-well plate and TaqMan array card assays
  • Filter based multimode plate readers
    • Molecular Devices Analyst HT equipped with stacker unit
    • Perkin Elmer EnVision equipped with liquid injector unit and 50-plate stackers
  • Microplate pipetting systems for handling serial dilutions and replication of plates for MOA studies
    • Agilent plate processing workstation – includes a Bravo liquid handler, BenchCell 4x with four stackers, a PlateLoc sealer, and Vcode barcode labeler; allows liquid dispensing using full-head and single-row or -column modes applicable for serial diluations
    • BioTek Precision – allows large-volume serial dilutions in 96- and 384-well plate formats and bulk dispense

Price List

For a Price List, please call (858) 646-3100 ext. 3462 or email us.

Leadership

Michael Jackson, PhD
Vice President, Drug Discovery & Development

Eduard Sergienko, PhD
Facility Director
esergien@sbpdiscovery.org

Contact

Please call (858) 646-3100 ext. 3462 or use the button below to send us an email.

Contact the Facility

Proteomics

close-up of scientist doing work in a lab

Overview

The Sanford Burnham Prebys Proteomics Shared Resource provides state-of-the-art mass spectrometry-based proteomics services including identification, quantification and characterization of proteins and their post-translational modifications. We provide proteomics services to Institute scientists as well as outside non-profit and for-profits organization on a fee-for-service basis.

The Proteomics Shared Resources is located on the main campus and currently houses three mass spectrometry platforms. The facility is run by four highly committed proteomics experts, including one faculty member as scientific advisor.

Equipment Highlight

Seer Bio Proteograph SP100
The platform combined with TMT multiplexing has the capability to detect ~2500 protein groups in plasma samples, including low abundant proteins like cytokines.

Seer Fact Sheet

Services

The Proteomics Shared Resource Offers a Diverse Array of Mass Spectrometry Services Including:

  • Identification and Localization of Post-Translational Modifications (e.g., phosphorylation, ubiquitinylation, acetylation, methylation, nitrosylation)
  • Quantitative comparison of protein abundances in complex mixtures using label-free or label-based techniques (e.g., SILAC, TMT)
  • Targeted protein identification and quantification  
  • Protein/Peptide Identification
  • Identification of protein-protein interactions by Affinity Purification followed by Mass Spectrometry (APMS) analysis
  • Identification of biotinylated proteins
  • Comprehensive serum proteomic profiling 

We urge you to consult with us prior to starting your proteomics experiment. We will help you to design the best experiment that fits your purposes.

Equipment & Resources

The Proteomics Shared Resource is equipped with 5 mass-spectrometry platforms, one automated liquid handling system for sample preparation and a robust computational infrastructure and software. Our mass spectrometers are coupled to either one- or two-dimension ultra-high performance nanoflow HPLC system (EASY nLC 1200, and 2D NanoAcquity).

Seer Proteograph XT

The Seer Proteograph XT is an advanced nanoparticle-based platform designed for deep, unbiased proteomics at scale. It enables high-throughput protein profiling with enhanced coverage, sensitivity, and reproducibility, making it a powerful tool for biomarker discovery and translational research. The platform enables the identification of over 3,000 proteins in human plasma, significantly expanding coverage compared to traditional mass spectrometry-based approaches.

Seer Fact Sheet

Orbitrap Fusion Lumos

The Thermo Scientific Orbitrap Fusion Lumos Tribrid is the newest state-of-the-art mass spectrometer that allows system biologists to test the limits of proteome analysis. It incorporates the brightest ion source, a segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology for improved ion transmission to the Orbitrap mass analyzer. These hardware improvements enable the new Tribrid instrument to excel in the most challenging applications, including analysis of low level proteins and PTMs, multiplexed relative quantitation using isobaric tags such as iTRAQ or TMT, and intact protein characterization. The Lumos is the most sensitive and versatile mass spectrometer currently available for proteomics work, and can do CID, HCD, and ETD fragmentation. Our two Lumos units are coupled to EASY 1200 UPLC system.

QExactive Plus

The QExactive Plus (QE+) is a highly sensitive, accurate mass instrument that uses an Orbitrap detector and HCD fragmentation. Our QE+ can be coupled to either a 2D M-Class NanoAcquity or an EASY 1200 UPLC system. With a fast scan speed and multiplexing capabilities, the QE+ is an outstanding system for mid-to-high complex proteomes. In addition, the QE+ also excels at targeted quantitation experiments, using the Product Reaction Monitoring (PRM) acquisition. In particular, we have developed an intelligent PRM approach which improves detection sensitivity at least 10x compared to conventional PRM method.

Orbitrap Elite

The Orbitrap Elite is a hybrid instrument consisting of an LTQ Velos Pro linear ion-trap coupled to a high-field Orbitrap detector. This allows high-mass accuracy scans to be acquired in the Orbitrap, and rapid sensitive scans to be acquired in the LTQ. The instrument can perform CID, HCD and ETD fragmentation. The high-field Orbitrap mass analyzer geometry and advanced signal processing technologies enable resolution of >240,000, superior spectral quality, and higher scan speed. The outstanding resolution increases analytical certainty by improving molecular weight determination for intact proteins and clearly resolving smaller, isobaric species. Our Orbitrap Elite is coupled to a EASY 1200 UPLC, and is generally used for low-to-mid complex proteomes.

Agilent AssayMap BRAVO Platform

For automated sample preparation

Price List

For a complete list of services, please call (858) 646-1000 ext. 4180 or email us.

Prod IDProteomics ServiceInternal
Subsidized		InternalExternal
Non-Profit		External
For-Profit
K800Total proteome profilingTMT 6plex$2,000$2,500$2,700$5,260
K801TMT 10plex$2,600$3,250$3,510$6,838
K802TMT 16plex$3,700$4,625$4,995$9,731
K015TMT 18plex$4,234$5,292.50$5,715.90$11,135.42
K803Phospho+Total proteome profilingTMT 6plex$3,100$3,875$4,185$8,153
K804TMT 10plex$3,600$4,500$4,860$9,468
K805TMT 16plex$4,943$6,178.75$6,673.05$13,000.09
K016TMT 18plex$5,560.88$6,951.09$7,507.18$14,625.10
K807Total proteome profilingLFQ$300$375$405$789
K808Total GoBig proteome profilingLFQ 6+$267$333.75$360.45$702.21
K809Phospho+Total proteome profilingLFQ 1x$500$625$675$1,315
K704Biotin AP-MS packageBioID$330$412.50$445.50$867.90
K705Biotin GoBig AP-MS package16+ BioID$300$375$405$789
K810On-bead’ AP-MS package1-5 samples$250$312$337.50$657.50
K8116+ samples$220$275$297$578.60
K812LC-MS/MS QE1-7 samples$170$212.50$229.50$447.10
K8138+ samples$150$187.50$202.50$394.50
K814LC-MS/MS Lumos1-7 samples$250$312.50$337.50$657.50
K8158+ samples$220$275$297$578.60

Leadership

Elena Pasquale, PhD
Scientific Director

Weiliang Huang, PhD
Facility Director
whuang@sbpdiscovery.org

Contact

Weiliang Huang, PhD, serves as the Director of the Proteomics Core and oversees the development, implementation, and delivery of advanced proteomics services to support biomedical research. He provides scientific leadership and guidance in experimental design, proteomic data acquisition, quantitative analysis, and interpretation of complex proteomics datasets. The core offers comprehensive proteomics capabilities, including label-free and isobaric labeling quantitative proteomics, post-translational modification analysis, protein enrichment and identification, interactomics studies, and bioinformatics support for large-scale proteomics data analysis. Dr. Huang works closely with investigators to develop tailored proteomics strategies and ensure high-quality, reliable, and impactful research outcomes.

Please call (858) 795-5052 ext. 5052 or use the button below to send us an email.

Contact the Facility

Metabolism

breast cancer in lymph nodes-nci

Overview

The Sanford Burnham Prebys Metabolism Core provides a hub within the Institute for analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All of the instruments and approaches are available on a fee-for-service basis to Cancer Center scientists, but also (as capacity permits) to outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.

Services

  • GC/MS or GC/MS/MS-based analysis of metabolites, including:
    1. Quantification of polar metabolites (such as amino acids, components of glycolysis and TCA pathways) in panels designed for different sample types (cells, medium, tumor/ tissue, serum/ plasma, or “total”) and including 39-89 metabolites.
    2. Stable isotope (13C, 15N, 2H) tracing of polar metabolites (25 metabolites)
    3. Fatty acids and cholesterol (quantification and 13C-tracing)
    4. Short-chain fatty acids (quantification with negative chemical ionization)
    5. Custom assays of sugars, sugar-phosphates, and related molecules
  • Quantification versus standards can be combined with stable isotope tracing. The combination can provide more confidence in identified changes in metabolic activity.
  • Measurement of cellular respiration and glycolysis using Seahorse XFp, XFe24 and XFe96 analyzers. These instruments determine rates of extracellular acidification and oxygen consumption by living cells respectively in a 6-well or larger 24 or 96 well formats. From these data, the relative activity of cellular glycolysis versus oxidative phosphorylation, including the balance of ATP production from these two major energetic processes, may be determined.
  • Measurement of major substrates and metabolites (glucose, glutamine, lactate, and glutamate) in culture medium using the YSI 2950 analyzer. This instrument is able to rapidly (~1 min per metabolite) determine the concentration of these important metabolism substrates from a small volume of sample (100-200 µL). Using a 96-well format, this analysis provides an economical method to roughly define changes in metabolism (e.g., in proliferating versus quiescent cells), and is also useful for checking that cells in culture have a sufficient supply of the major nutrients glucose and glutamine.

Equipment & Resources

  • A Thermo TSQ 9610 gas chromatograph- triple quad mass spectrometer (GC-MS/MS) is used for quantitative analysis of up to 90 polar metabolites from samples including cells, tumors or serum. It is also used for quantification of fatty acids and short-chain fatty acids (SCFA). SCFA are analyzed with negative chemical ionization, which reduces background and allows for low detection limits.
  • A Shimadzu QP2010 GC-MS is used for metabolic analyses which include determination of stable isotope (13C, 15N) labeling rates of intra- and extracellular metabolites. 13C labeling can be measured in amino acids, keto and fatty acids, sugars, and sugar phosphates. 
  • The YSI 2950 metabolite analyzer is able to measure glucose, glutamine, lactate and glutamate in media in 2-3 minutes for all 4 metabolites in a 96-well format. The minimum volume needed is 100 μl. A full 96-well plate may be analyzed in 3-4 hours and results are typically returned the same or next day.
  • The XFp Analyzer can measure respiration in most cell types, including primary cells, adherent cells, and suspension cells (with attachment). With a 6 well format, the XFp Miniplate is ideal for pairwise comparisons (in triplicate) and the analysis of precious samples, such as patient-derived and other rare samples. We mainly focus on the Cell Mito Stress Test to measure the key parameters of mitochondrial function: basal respiration, ATP production, proton leak, maximal respiration, and spare respiratory capacity. Other protocols to measure the use of alternate substrates or to calculate the relative production of ATP from glycolysis or oxidative phosphorylation are available.
  • The XFe24 Analyzer is similar to the XFp, but well sizes are 2.5x larger and up to 22 samples can be run on one plate. We have available islet capture plates.
  • The XFe96 analyzer has the same well size as the XFp and can run up to 92 samples on one plate.

Price List

For a complete list of services, please call (858) 646-1000 ext. 3941 or email us.

Cancer Metabolism ServicesInternal
(Subsidized)		Non-ProfitFor ProfitMinimum
sample
number		Code
GCMS metabolite quantification and stable isotope (13C) tracing (per sample)
Polar metabolite GCMS quantification (Simpler: cells, medium, plasma, tissues)$48$64.80$126.2412CMR162
Polar metabolite GCMS quantification (Complex: cecum, feces, urine)$54$72.90$142.0212CMR183
Polar metabolite 13C GCMS analysis$48$64.80$126.246CMR163
Combined GCMS 13C & quant polar metabolites$91$122.85$239.338CMR170
Fatty acid & cholesterol GCMS analysis (quantification)$54$72.90$142.0212CMR164
Fatty acid 13C GCMS analysis$52$70.20$136.766CMR171
Combined GCMS 13C & quant fatty acids$99$133.65$260.378CMR184
Short-chain fatty acid GCMS quantification$56$75.60$147.2812CMR172
Sample prep for GC-MS (extra to sample analysis fee)
Sample prep – cells or medium, or serum/plasma$4$5.40$10.52N/ACMR175
Sample prep – fecal/cecum; weighed tumor or tissue$10$13.50$26.30N/ACMR177
Sample prep – tumor, tissue, not weighed or needs re-weighing$15$20.25$39.45N/ACMR176
Sample prep – urine with urease treatment$6$8.10$15.78N/ACMR174
Charges for Seahorse analyzers and YSI Bioanalyzer
Seahorse XFp (per plate) (training/full service)$200$270$526N/ACMR166
YSeahorse XFp (per plate) (self-service)$80$108$210.40N/ACMR168
Seahorse XFe24 (per plate) (training/full service)$345$465.75$907.35N/ACMR178
Seahorse XFe24 (per plate) (self-service)$210$283.50$552.30N/ACMR179
Seahorse XFe96 (per plate) (training/full service)$345$465.75$907.35N/ACMR180
Seahorse XFe96 (per plate) (self-service)$230$310.50$604.90N/ACMR181
YSI metabolite analysis (per plate)$115$155.25$302.45N/ACMR167
Notes

Sample prep charges (CMR174-177) are for sample extraction for GCMS, and are in addition to the GCMS charges. If samples are submitted as dried extracts the prep charges will not apply. See core for details.

25% discount for samples for GCMS in excess of 30 in a single batch, rounded to nearest sample (e.g., 32-35 samples, discount of 1 sample).

Self-service rate for Seahorse analyzers includes the cost of plates, XF-medium and reagents.

Leadership

Brooke Emerling, PhD
Scientific Director

David Scott, PhD
Facility Director
dscott@sbpdiscovery.org

Contact

David Scott focuses on the development and application of methods for metabolomics, enhanced by the use of stable isotope substrates. Stable isotopes (mainly 13C) provide an added layer of information to metabolomic studies – not only is static pool information obtained, but it is also possible to infer the origins of metabolites and to track flux through metabolic pathways. Methods used include the analysis of small polar metabolites (mainly amino acids and carboxylic acids) and fatty acids by gas chromatography-mass spectrometry. Other techniques are being developed to analyze and quantify an expanded range of (labeled) metabolites. We have applied these methods in a study of the central carbon metabolism in Escherichia coli, and, in several papers, on melanoma metabolism. Investigations of melanoma cells showed the importance of glutamine metabolism under hypoxia, identified a novel route for the utilization of the carbon backbone of glutamine for fatty acid synthesis, and defined pathways for proline synthesis. Other recent work uses alternately labeled sugars to simultaneously track different inputs to glycans in normal cells and cell lines from patients with glycosylation defects.

Please call (858) 646-3100 ext. 3941 or use the button below to send us an email.

Contact the Facility

Viral Vectors

close-up of rotovirus cells

Overview

The viral vector core facility at Sanford Burnham Prebys develops state-of-the-art viral vector-based gene delivery technology. Its portfolio ranges from lentivirus, retrovirus, adenovirus, AAV, VSV, sindbis virus, and Zika virus products as well as customized “The Works” viral vector construction and swapping service package. There are a variety of ready-to- transduce viral vector collections including constitutively expressed or inducible fluorescent proteins for nuclear or membrane localization and bioluminescence reporters for 3D drug screening. The viral core has integrated CRISPRs/Cas technology in the plasmid-free viral vector platform, providing scientists with choices of combined technologies to manipulate genes using CRISPR gene disruption, editing, inhibition, and activation. In addition, we extend technical expertise in nanoparticle research including exosome purification, analysis, and engineering. More importantly, the core actively participates and supports translational research to fight human diseases.

Services

  1. Custom large scale rAAV production and titration. Serotypes include 1-9, 3B, 7M8, shH10, DJ, DJ/8, PHP.B, PHP.eB, PHP.S, B1, rh10, Anc80, and Retrograde. Ready-to-transduce rAAV-CMV-eGFP and CAG-NLS-eGFP/mCherry viruses are available upon request.
  2. Custom large scale lentiviral [HIV-1, integrase defective lenti-virus (IDLV), and FIV] and retroviral (MSCV and MMLV) production and titration is based on vector plasmid DNA provide by the user. Titration is offered for virus ubiquitously expressing fluorescence or puromycin selection marker.
  3. Ready-to-transduce lentiviral preps include: (1) doxy-inducible or constitutively expressed cytoplasmic fluorescent reporters w/out mammalian selection markers (2) nuclear or membrane localized fluorescent reporters (3) secreted or cytoplasmic bioluminescent reporters (4) doxy-inducible or constitutively expressed non-silencing control (scramble) shRNA (5) cell cycle and autophagy reporters.
  4. Custom large scale adenoviral particles (Ad5) production and titration from user-supplied construct or virus include: (1) adenovirus recovery (2) high purity adenoviral preparation using CsCl gradient purification (3) titration via plaque assay. Ready-to-transduce pAd5-eGFP, NLS/CAAX fused eGFP/mCherry, firefly or secreted gaussian/cypridina luciferase, and Cre recombinase viruses are available upon request.
  5. “The Works” custom lentiviral-adenoviral-rAAV vector construction and swapping include:
    1. Doxy-inducible or constitutively expressed cDNA or shRNA
    2. Promoter / enhancer reporter (3) microRNA sponges
  6. siRNA to lenti shRNA vector conversion with choice of doxy-inducible H1 or constitutive hU6 promoter as well as puromycin or neomycin selection marker. Ready-to-transduce non-targeted siRNA converted or universal scramble shRNA lentiviruses are available upon request.
  7. Custom packaged Sindbis virus production and titration. Ready-to-transduce mCherryCAAX-eGFP virus, pSINREP5-based vector construction, packaging, and flow cytometry-based titration are available upon request.
  8. Custom VSV vector construction, production, and titration. Pseudotyped VSV-ΔG-eGFP with Ebola virus glycoprotein (EboV-GP) Zaire strain (Kissidougou-C15, 2014) or wild-type VSV glycoprotein (VSV-G) are available upon request.
  9. Custom Zika virus production and titration are available for African, Asian, and Brazilian (2015-2016 outbreak) strains.

Equipment & Resources

The Core is fully equipped with all the necessary equipment for production of consistent quality viral vectors including state-of-the art cell culture hoods and incubators under appropriate biosafety conditions, as well as an ultracentrifuge, microscopes and a dedicated -80°C freezer for storage of vectors. Producer cell lines 293T and 293A cells are routinely tested for the presence of mycoplasma using Lonza detection kit and discontinued at passage 20.

The Institute is in a partnership program with Sigma-Aldrich and Open Biosystems. Both companies provide affordable shRNA constructs. The Core also currently collaborates with Dr. Terskikh and Dr. Mercola labs to increase ready-to-transduce virus inventory.

Our lab uses the Cytocentric Xvivo System from BioSpherix Ltd to aseptically control O2, CO2, and temperature levels during the incubation, handling, and analysis of live cells without the disturbances which routinely occur in traditional cell culture incubators. This platform allows our core users to more accurately recapitulate physiologic, in vivo-like conditions during in vitro experiments with living cells. More information can be found at: biospherix.com/xvivo-system-model-x3

Price List

For a Price List, please call (858) 646-3100 ext. 4353 or email us.

Leadership

Chun-Teng Huang
Associate Director
cthuang@sbpdiscovery.org

Ching-Lien Fang
(858) 646-3100 ext. 3803

Contact

Please call (858) 646-3100 ext. 3803 or use the button below to send us an email.

Contact the Facility

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.
  • Epigenomics: Full-service epigenomic profiling from cells, including CUT&RUN, CUT&TAG, TIP-CHIP, and ATAC-seq for chromatin accessibility and protein-DNA interaction analysis.
  • 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 at rporritt@sbpdiscovery.org.

Services

Next-Generation Sequencing (NGS)

We offer full-service library preparation and sequencing on the Element Biosciences AVITI24 platform, which provides industry-leading accuracy at competitive pricing. With dual independent flow cells and a 1.5B read capacity, the AVITI enables high-throughput sequencing for RNA and DNA libraries. Flexible flow cell configurations available.

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&RUN
  • 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

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

Contact the Facility