Genomics and High-Throughput Screening Shared Resource (HICCC)
The Genomics and High-Throughput Screening Shared Resource (GHTSSR), jointly managed by the Herbert Irving Comprehensive Cancer Center and the Department of Systems Biology, provides access to specialized instrumentation and technical expertise in three highly complementary service components: (1) RNA and DNA next-generation sequencing (NGS), (2) single-cell RNA-seq, and (3) high throughput and high-content microscopy-based screening of chemical, RNAi, and cDNA libraries. Directed by Olivier Couronne, PhD, MBA, the GHTSSR is broadly used and highly regarded by investigators for its reliability, advanced capabilities, and a high-level of technical innovation. Highly qualified personnel in the GHTSSR facilitate effective use of these advanced technologies.
The GHTSSR sequencing services (RNA-seq, genome-wide DNA [whole exome, whole genome, ChIP-seq, and ATAC-seq] and targeted DNA sequencing) are of high-quality, readily accessible, affordable, and are performed in a timely manner. Comprehensive single-cell RNA-seq services make this complex technology highly accessible and a critical resource for research programs studying cellular heterogeneity and plasticity, and the complex microenvironments. Similarly, the high-throughput screening, high content microscopy component of the GHTSSR supports both basic and translational biomedical research by assisting investigators in the development, optimization, and execution of high-throughput assays that deliver answers to questions of scientific interest. The supported screening platforms are tailored to meet the specific needs of investigators and include innovative sequencing-based high-throughput screening technologies such as PLATE-Seq that are not available commercially or at other academic centers. Medium-throughput molecular screening (MTMS) is also available through on-demand access to dedicated state-of-the-art equipment such as the Fluidigm BioMark HD and the Fluidigm C1.
The GHTSSR occupies 2,200 square feet of space in the Lasker Biomedical Research Building.
Equipment
- Illumina NovaSeq 6000 System
- Illumina NextSeq 500 and 550 (3)
- Illumina MiSeq
- 10X Genomics Chromium Single Cell 3’ System
- Beckman Coulter Biomek 4000 Automated Workstation
- Perkin Elmer Cell Explorer
- Perkin Elmer Janus
- Hamilton Microlab STAR liquid handling system
- Labcyte Echo 550
- General Electric InCell 2000
- GE Biacore X100 system
Next generation sequencing: In 2018, the GHTSSR updated from the Illumina HiSeq 4000 to the NovaSeq 6000, the newest very high-throughput next-generation sequencing instrument capable of sequencing up to 10 billion reads in one day long run. This instrument provides an unprecedented throughput at the lowest cost per sample. The Illumina NextSeq 500 and 550 (3 instruments) provide benchtop mid-throughput and high-throughput next-generation sequencing, with fully integrated workflows from library preparation to data analysis, report generation, and data sharing. All our users have complete access to these instruments. The Illumina MiSeq is a next-generation sequencing instrument for targeted resequencing, metagenomics, small genome sequencing, and targeted gene expression profiling with long reads up to 2x300bp.
Single cell RNAseq: The GHTSSR provides services using two single-cell RNA-seq platforms: the 10x Genomics Chromium 3’ Solution and pooled scRNA-seq in 96-well plates. The 10x Genomics Chromium Single Cell 3’ platform encapsulates thousands of individual cells in droplets for lysis and reverse transcription from up to 8 samples in parallel. Each droplet contains primers for cell- and molecule-specific barcoding of cDNA. CUIMC investigators provide live cells or nuclei in suspension to a SR technician for loading and automated generation of pooled 3’-end cDNA libraries for sequencing on the Illumina NovaSeq platform. The Biomek 4000 Automated Workstation - Beckman Coulter, a compact liquid handler enabling standardized pipetting routines supportsin plate scRNA-seq. The GHTSSR provides services using the 10x Genomics Chromium Single Cell ATAC-Seq Solution. This platform transposes nuclei in a bulk solution; then using a microfluidic chip, the nuclei are partitioned into droplets to uniquely index the transposed DNA of each individual nucleus. CUIMC investigators provide nuclei in suspension to the core. Libraries are sequenced on the Illumina NextSeq 500/550.
High Throughput Screening and High Content Microscopy: The Perkin Elmer Cell Explorerautomated system, uses an anthropomorphic robotic arm to transport microtiter plates from one module to another. It also includes sophisticated instrumentation and software to limit variance among wells during assay preparation and plate incubation. This helps to ensure the accuracy of the data that result from each assay. Major instruments integrated into the Cell::Explorer are: the Perkin Elmer Janus liquid handling instrument with swappable 96 channel, 384 channel and nano head, Perkin Elmer EnVision multilable plate reader with enhanced luminescence, Certus dispensing system, Agilent Microplate Centrifuge, Agilent VCode plate barcoding system, BioTek Select 405 plate washer, Liconic StoreX 1000 compound storage system and Liconic StoreX 500 Tissue Culture Incubator. The Hamilton Microlab Star was obtained for functional genomics assays. The system contains a 96 well pipetting head as well as an independent 8-channel pipetting system; the deck contains positions for heating and cooling microtiter plates. This system is used to process plates for PLATE-Seq. Labcyte Echo 550 is an acoustic liquid handling system, integrated into an Access workstation (Precision Automation Inc.) for complex liquid handling problems. The Access workstation contains 4 plate stacks along with plate de-liders and barcode readers, allowing for the high-throughput processing of plates in the Echo system. The General Electric InCell 2000 is used for high throughput microscopy-based assays, equipped with a large CCD camera, capable of whole-well imaging in 96- or 384-well microplates. The InCell 2000 has imaging modes, which enables users to get confocal-like quality in a high-throughput experimental setting. The instrument has been integrated with a Mitsubishi robotic arm and a Cytomat plate hotel to expand the throughput of fixed cell assays. The GE Biacore X100 system, obtained in 2017, is a surface plasma resonance system which can be used to determine protein/protein, protein/antibody or protein/small molecule interaction. The Biacore system is the only system that allows users to run single cycle kinetic studies.
Small molecule libraries: The shared resource contains numerous small molecule libraries of both known drug/bioactive and novel synthetic compounds. The two largest bioactive libraries are the MicroSource Spectrum collection and the Prestwick library. These libraries each contain a significant number of known drugs and biologically active small molecules, making them ideally suited for new assay development and molecular perturbation experiments. In addition to the libraries of known drugs, the center has expanded their diversity libraries with the addition of two new libraries: The Lead Optimization Collection (LOC), which contains 10,000 unique small molecules, and the Enamine Library, which contains over 60,000 unique small molecules. Additionally, 10,000 unique, natural product-like compounds are available from the center’s Analyticon NatDiverse Library; 2,000 natural products from Analyticon’s Natural Product Library; 26,793 compounds from Life Chemicals; 90,000 compounds from ChemBridge; and 70,941 compounds from ChemDiv. In addition, there are libraries of siRNA’s from Dharmacon including targeted libraries of Drug Targets, GPCRs, Ion Channels, Phosphatases, Proteases, Kinases and Ubiquitin Conjugation Subsets. Columbia has also entered into agreement to get low cost access to lenti-viral shRNA’s from Sigma Aldrich as both glycerol stocks and virus particles. For overexpression assays, the Precision LentiORFs collection is available through the GHTSSR. The HTS/HCM has also implemented sophisticated bioinformatics management software and analytical platforms, including Pipeline Pilot, Chemical/Biological Registration, and BioRails from Accelrys.
Standards, Rigor, and Reproducibility
Quality control procedures recommended by the instrument manufacturer are in place to ensure proper instrument operation. To ensure rigor and reproducibility, all analytical services include standard operating protocols (SOPs), are updated annually, and are routinely validated using technical replicas.