Genomics and High Throughput Screening

  • Olivier Couronne, PhD
    • Director
  • Aris Floratos, PhD
    • Director, Bioinformatics
  • Charles Karan, PhD
     
    • Scientific Director, High Throughput Screening 

The Genomics and High Throughput Screening Shared Resource is operated jointly by the Herbert Irving Comprehensive Cancer Center and the Judith P. Sulzberger Columbia Genome Center. The facility provides access to specialized instrumentation and technical expertise in three highly complementary service components:

  • Next-generation (Nextgen) Sequencing
  • High-Throughput Screening, High Content Microscopy (HTS/HCM)
  • Medium-throughput Molecular Screening (MTMS)
  • Single Cell Analysis Core

The JP Sulzberger Columbia Genome Center

To learn more about the Genomics and High Throughput Screening Shared Resource, including user policies, pricing, and to request a consultation, please visit the Judith P. Sulzberger Columbia Genome Center.

Visit the Judith P. Sulzberger Columbia Genome Center


Next-generation (Nextgen) Sequencing

Next-generation DNA sequencing and RNA-seq have made it possible not only to look at individual genomes, but also to rapidly compare genetic sequences among multiple genomes. As next-generation sequencing technologies have made it possible to generate high-resolution genomic data much more efficiently, researchers in many fields have turned to next-generation sequencing to identify particular features of the genome that contribute to specific phenotypes.

Instrumentation

  • Illumina HiSeq 4000
  • Illumina HiSeq 2500
  • Illumina NextSeq
  • Illumina MiSeq

For Services

For queries regarding Nextgen sequencing, please contact genome@columbia.edu.


High-Throughput Screening, High Content Microscopy (HTS/HCM)

The HTS/HCM component of the Genomics Shared Resource 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. A unique way in which these technologies are used is to perturb cellular systems to dissect their regulatory mechanisms and the mechanism of action of small-molecule and genetic perturbations.

Instrumentation

  • Automated Technology Platforms
    • PerkinElmer cell::explorer
    • HighRes Biosolutions workstation
    • Hamilton Microlab STAR
    • Beckman Coulter Echo dispensing system
  • Microplate Reading Technologies
    • PerkinElmer EnVision 2104 Multilabel Microplate Reader
    • Tecan Infinite M2000 Pro
  • High-content Microscopy Instrumentation
    • GE Healthcare IN Cell Analyzer 2000

For Services

For queries regarding high-throughput screening and high-content microscopy, please contact Ck2389@cumc.columbia.edu


Medium-throughput Molecular Screening Instrumentation

The Genomics SR provides access to dedicated state-of-the-art equipment for medium throughput biological assays. These instruments allow investigators to perform sophisticated, multiplexed measurement of gene and protein expression, allowing for direct, quantitative measurement of mRNA, miRNA, and protein abundance.

Instrumentation

  • Fluidigm BioMark HD
  • Fluidigm C1 Single-Cell Autoprep System

For Services

For queries regarding medium-throughput molecular screening, contact contact genome@columbia.edu.


Single Cell Analysis Core

The Single Cell Analysis Core provides experimental and computational support for single-cell RNA-Seq (scRNA-Seq) and single-cell ATAC-Seq (scATAC-Seq). We offer services using two scRNA-Seq platforms and an scATAC-Seq platform.

Instrumentation

  • 10x Genomics Chromium Single Cell Controller
  • Beckman-Coulter Biomek 4000
  • ThermoFisher Countess II FL Automated Cell Counter
  • Miltenyi gentleMACS Octo Dissociator

For Services

For queries regarding single cell analysis, contact genome@columbia.edu.


Bioinformatics Core

Services

Data analysis and database access services

These help HICCC investigators create preliminary data for research grant proposals and final data for publications and presentations. For instance, an often requested service includes normalizing and analyzing high-throughput sequencing data (RNASeq, ChIPSeq, ATACSeq), microarray data (expression profiles, ChIP on chip, genotyping, etc.), or proteomic data and then uploading it in standard repositories, such as GEO (Gene Expression Omnibus). Use of appropriate statistical tests and data mining tools, reflecting accepted best practices, is a key element of success in proposal and publication submissions. Other services include gene identification and molecular modeling.

Access to a variety of public and commercial bioinformatics web-tools

Which tools (or tool sub-functionality) to use to address a specific problem is a complex question, with answers that are in constant evolution. The BISR personnel help investigators select from a vast array of available tools the ones that best fit their requirements and reflect accepted best practices or specific publication requirements.

geWorkbench Integrated Genomics Web Site

Bioinformatics Web Sites

Custom bioinformatics workflow development

Although the typical experimental lab may have the ability to use bioinformatics software, given appropriate access and training, the ability to program customized data analysis workflows, to integrate multiple tools, is extremely rare. A typical example is the intersection of ChIP-on-chip and gene expression profile data, followed by sequence analysis to identify functionally active DNA binding sites for a given transcription factor. The BISR addresses this need by providing custom programming expertise. Over 80 papers have resulted from these collaborations.

Custom biological database development

An increasing number of HICCC investigators are producing high-throughput biological data, which often require stratification according to phenotypic information in clinical databases. The BISR helps investigators to develop and to host their custom databases and to integrate them with those containing clinical data.

Custom web site development for data sharing and dissemination

Based on the data sharing plan and on increasingly strict requirements from journals, HICCC investigators must share and disseminate their results to the research community. This is usually done using either an access controlled or an unrestricted access web portal. BISR personnel help design, develop, deploy, and host these portals in a more efficient and cost effective way than if they had to be developed and maintained by the individual HICCC investigator.

Access to high performance computing equipment for computationally intensive analyses

New generation bioinformatics tools, especially in the area of systems biology or when large genomic data scans are required, may require substantial computational power and storage requirements. Traditionally, research labs would either purchase and maintain their own hardware or seek collaboration with bioinformatics collaborators who can run these computationally intensive programs. The BISR has access to one of the largest academic computational clusters dedicated to research in molecular and systems biology.

User Fees and Policies

All data analysis, support, consulting, and web site development services:

  • Cancer Center Members: First 3 hours free; $90/hour thereafter
  • Non-Cancer Center Members: First 3 hours free; $120/hour thereafter
  • External users: $192/hour

Access to High Performance Computing Equipment

Access to cluster computing resources are available to users of the biomedical informatics shared resource through the department of Systems Biology.

Details about infrastructure and usage fees can be found at the Department of Systems Biology website.

Online Reservations

The Biomedical Informatics Shared Resource uses the iLab Core Management System for service requests and billing. Before you can request services, you must log into iLab and be approved as a lab member.

Affiliate Organizations

Department of Systems Biology

Department of Biomedical Informatics

Center for Cancer Systems Therapeutics (CAST)


Locations and Contact

High-Throughput Screening

(also includes queries regarding high-content microscopy)

JP Sulzberger Columbia Genome Center

High-Throughput Screening Center

Mary Woodard Lasker Biomedical Research Building

3960 Broadway; Room 330

New York, NY 10032

Contact: ck2389@cumc.columbia.edu

Genome Sequencing and Analysis

JP Sulzberger Columbia Genome Center

Genome Sequencing and Analysis

Mary Woodard Lasker Biomedical Research Building

3960 Broadway, Room 208 (entrance on W. 166th St.)

New York, NY 10032

Contact: genome@columbia.edu

Single Cell Analysis Core

JP Sulzberger Columbia Genome Center

Genome Sequencing and Analysis

Mary Woodard Lasker Biomedical Research Building

3960 Broadway, Room 208 (entrance on W. 166th St.)

New York, NY 10032

Contact: genome@columbia.edu

Bioinformatics Core

Aris Floratos, PhD, Director 
Tel: (212) 851-5139
Email:  af2202@cumc.columbia.edu
Irving Cancer Research Building, Room 801,
1130 St. Nicholas Avenue, New York, NY 10032

Richard A. Friedman, PhD
Specializing in gene expression analysis, functional, sequential, and structural genomics, and proteomics, biostatistics, and microbiomics.
Tel: (212)851-4765
Email: raf4@cumc.columbia.edu
Irving Cancer Research Building, Room 825,
1130 St. Nicholas Avenue, New York, NY 10032