Functional Genomics - Sanford Burnham Prebys

Functional Genomics

A scientist works with lab equipment

Overview

The Sanford Burnham Prebys Functional Genomics and Viral Vector Shared Resources provide comprehensive infrastructure and expertise for high-throughput genomic screening and gene delivery. The facility supports cell-based gain-of-function (ORF, CRISPRa/CRISPRon) and loss-of-function (siRNA, miRNA, shRNA, CRISPR-KO, CRISPRi/CRISPRoff) studies, encompassing assay development, reporter cell line engineering, large-scale genome-wide or pathway-specific library screening (arrayed or pooled formats), and validation of identified targets. Advanced capabilities include CRISPR gene editing, activation, and repression, as well as nucleotide base editing and tiling approaches to interrogate gene function, protein domains, and drug-target interactions.

High-throughput automation enables DNA purification, plasmid quantification, virus production, and custom assays in 96- and 384-well formats using our NIH S10-funded Biomek i7 Hybrid Automated Workstation (OD036254). Complementing these capabilities, the Viral Vector Facility offers a broad range of gene delivery platforms, including lentivirus, retrovirus, adenovirus, adeno-associated virus, and other viral systems, along with customizable vector design services. The core produces high-titer viral particles for in vitro and in vivo applications and provides over 50 ready-to-use reporter viruses for imaging and 2D/3D assays. Additional expertise includes non-viral nanoparticle technologies, such as extracellular vesicle and exosome purification, analysis, and engineering.

Together, these integrated resources enable scalable functional genomics studies and advanced gene delivery approaches to accelerate discovery of gene function, mechanisms, and therapeutic targets.

Services

  1. siRNA library preparation and arrayed screen
    The core has genome-wide human siRNA library ON TARGET-Plus (OTP) library (18,301 genes, Dharmacon (Dh) / Thermo Scientific (TS)), formatted as SMARTpools and 4 single siRNAs per gene. Seventeen collections of pre-spotted pathway-focused libraries include (1) druggable genome (7740 genes, Applied-Biosystems (AB) / Life Technologies (LT)); (2) epigenetics / transcriptional-regulators (1362 genes, AB/LT); (3) epigenetics (882 genes, created by SBP in-house); (4) ubiquitinome (1170 genes, Qiagen and 1432 genes, SBP); (5) kinome (704 genes, AB/LT and 831 genes, SBP); (6) cancer pathway (252 genes, Dh/TS); (7) phosphatases (231 genes, Dh/TS and 314 genes, SBP); (8) G protein coupled-receptor (GPCR) (Dh/TS); (9) metabolome (160 genes, AB/LT); (10) miniscreen random subset (Dh/TS); (11) autophagy (1601 genes, SBP); (12) innate immunity (96 genes, SBP); (13) B cell activation (127 genes, SBP); (14) T cell activation (287 genes, SBP); (15) ion channel (380 genes, SBP); (16) apoptosis (823 genes, SBP). Customized siRNA cherry-pick service is available upon request. In addition, CRISPR/Cas9 arrayed screening with (17) kinome gRNA library (789 genes, TS) is available.
  2. miRNA mimic and antagonist library arrayed screen
    The core has human miRNA mimic library (875 miRNAs from miRBase sequence database Version 10.1., AB/LT) and miRVana library (2565 miRNAs, TS). Libraries of miRNA antagonist include human miRIDIAN miRNA inhibitor (885 anti-miRNAs from miRBase 13.0 release, Dh/TS), Exiqon miRCURY LNA™ Inhibitor and microRNA Family Inhibitor (Qiagen). Collections of pre-spotted autophagy pathway-focused libraries include miR mimics (259 mimics, SBP) against autophagy-related genes and miR antagonists (255 antagonists, SBP) targeting autophagy-related miRNAs.
  3. Lentiviral shRNA and open reading frame (ORF) overexpression library arrayed screen
    The core has RNAi Consortium (TRC) lentiviral kinome shRNA library (SIGMA) covering 672 kinases and regulators with an average of 11 shRNAs per target. 2440 sequence verified ORFs from the Ultimate ORF Collection (LT) are available as sub-libraries including secreted protein (858 ORFs), apoptosis (476 ORFs), kinase (373 ORFs), and innate immunity (172 ORFs).
  4. CRISPR/Cas genome-wide / sub- library preparation and arrayed/pooled screen
    The Core has acquired a portion of the CRISPRa T. gonfio library, including kinase, phosphatase, and drug target genes (2,012 genes), from Dr. Aguzzi’s group at UZH and has generated arrayed bacterial, plasmid DNA, and lentiviral libraries. Additionally, the core has obtained CRISPR lentiviral pooled libraries from Addgene, including two human genome-wide (GW) knock-out (KO) (Root and Doench, Zhang labs), one mouse GW KO (Teichmann lab), three human GW activation (Root and Doench, Weissman, Zhang labs), and two human GW inhibition libraries (Root and Doench, Weissman labs). Human pathway-focused pooled libraries contain (1) CRISPR/Cas9 KO sub-libraries of kinases; cell cycle proteins; nuclear proteins; unknown function; control targets (Sabatini and Lander lab) and (2) CRISPR/dCas9 inhibition sub-libraries of kinases, phosphatases, and drug targets; stress and proteostasis; mitochondria, trafficking, and motility; gene expression; membrane proteins (Weissman lab) as well as (3) SBP unpublished CRISPR/Cas9&Cas12 KO sub-libraries of kinome; epigenetics; ubiquitome; autophagy; phosphatase; ion channel; cancer pathway; innate immunity developed in-house. Furthermore, the core offers custom pooled single, dual (Cas9), triple (Cas12a), and quadruple (3 Cas12 + 1 Cas9 or 4 Cas12) gRNA(s) library construction services.
  5. Custom CRISPR/Cas gene disruption and editing
    The core provides custom creation of isogenic cell lines including gene knock-out, mutation and repair, as well as reporter insertion. Approaches to express CRISPR include lentiviral transduction and transient transfection with in vitro transcribed (IVT) RNA. Moreover, custom genetic modified mouse creation is accomplished via Rosa26 loci knock-in on C57BL/6 C2 and 129 mESCs.
  6. High-activity CRISPR/Cas stable cell line enrichment
    To avoid clonal line screening, the core has developed multiple fluorescent reporters capable of bulk-sorting to enrich lentiviral-transduced cells with high-efficiency SpCas9 and EnAsCas12a for CRISPRko; SpnCas9-ABE, CBE and A&CBE for CRISPR DNA adenine (A) and cytosine (C) base-editing (BE); dCas9-effectors for CRISPRon/off.
  1. Custom gene knock-down and overexpression via CRISPR inhibition, activation, on and off
    Repurposing CRISPR/Cas9 for promoter/enhancer regulation allows any gene and particularly long non-coding RNA (lncRNA) to be (1) inhibited through CRISPRi-dCas9-Krab (Weissman lab) or CRISPRoff-dCas9-Krab-DNMT3 (Gilbert lab) and (2) activated via three available CRISPRa-dCas9-VP64 systems, including SAM (Zhang lab), suntag (Weissman lab), and split fluorescent protein (Huang lab) as well as CRISPRon-TETv4 (Gilbert lab).
  1. NGS-ready amplicon library preparation and quality control
    The core is equipped with Dual Index Primers Set (NEB) which is compatible with Illumina NGS platform and capable of multiplexing up to 96 pooled amplicon libraries. Multiple quality control procedures are integrated to ensure the library complexity and quality during the amplification.
  1. Automated mini-scale production
    The robotic high throughput mini-scale services include clonal cell line creation, mammalian genomic DNA extraction, plasmid DNA isolation, DNA quantification and normalization, as well as lenti-/retro-viral production in 96-well plate format.
  1. Cell population barcoding
    Retrievable barcode technology such as CloneTracer barcoding lentiviral pooled library (Stegmeier lab) is available to create individually barcoded cell populations for linage tracing. Monitoring the unique barcode and number of individual barcode provides a quantitative analysis to study the clonal origin and heterogeneity in cell proliferation, differentiation, as well as resistance to the drug treatment
  1. Viral Vectors-based gene delivery technology

Equipment & Resources

See Services for a list of libraries

  • Benchcell work station with Bravo liquid handling platform (Agilent)
  • STAR liquid handling station (Hamilton)
  • Tissue culture facility
  • WellMate liquid dispenser (Matrix Technologies)
  • Micro Flo Liquid Dispenser (BioTek)
  • ELx 405 Plate washer (BioTek)
  • High-Throughput Microscopes and Plate Readers are utilized via the High Throughput Screening and High Content Screening
  • Biomek i7 Hybrid Automated Workstation (Beckman Coulter), funded by S10 OD036254
  • CloneSelect Imager (Molecular Devices)

Price List

For a Price List, please call (858) 646-3100 ext. 3537 or email us.

Leadership

Ani Deshpande, PhD
Scientific Director

Chun-Teng Huang
Associate Director
cthuang@sbpdiscovery.org

Contact

Please call (858) 646-3100 ext. 4353 or use the button below to send us an email.

Contact the Facility