UCCRC Core Facilities: Genomics

Scientific Director:   T. Conrad Gilliam, PhD

Technical Directors: William J. Buikema, PhD, and Rafael Gama, PhD, Barry Allen, PhD

DNA Sequencing and Genotyping:               
http://cancer-seqbase.uchicago.edu
Phone:  773-702-1088

Functional Genomics Facility:   
http://fgf.bsd.uchicago.edu
Phone: 773-834-8420

Biomedical Research Development Facility
http://brdfhelp.uchicago.edu
Phone:  773-649-6435

The Genomics Core Facility provides, via its three Subcores, state-of-the-art microarray, DNA sequencing, and genotyping platforms with specialized databases for storing, managing, and manipulating both clinical information and diverse types of genetic and genomic data.  The Facility is aimed towards both biomedical researchers who are generally unfamiliar with whole genome and bioinformatics approaches, as well as experts seeking sophisticated hardware, software, programming, or database solutions, or seeking to facilitate interdisciplinary collaborations.  The Facility maintains the latest copies of all major genomic databases, thus allowing investigators to perform all genomic and bioinformatics analyses at the highest possible speeds.

Services

DNA Sequencing and Genotyping:

  • Full-service:  DNA sequencing of plasmid and PCR templates, including reactions, cleanup, and capillary electrophoresis;
  • Abbreviated-service:  Electrophoresis of DNA sequencing and genotyping reactions provided by users (e.g. fragment analysis, SNAPSHOT and SNPlex);
  • Genotyping analysis on the Sequenom MassARRAY system;
  • Colony picking, 96-well cell culturing, plasmid preparation, and preparation of glycerol stocks;
  • Plate genotyping by fluorescence polarization (e.g. SBE-FP genotyping), fluorescence intensity (e.g. TaqMan genotyping), and plate luminometer readings for promoter analysis and picogreen DNA concentration assays (all performed by users at no charge);
  • Fragment assembly and primer walking;
  • Data analysis services:  GeneMapper for genotyping analysis and Sequencher for editing and alignment of chromatograms; and
  • Technical consultations for DNA preparation and interpretation of results and archival data storage (provided at no charge).

Functional Genomics Facility:

  • Pre-experiment consultation:  Advice on individual experimental design and validation of protocols for University of Chicago investigators (provided at no charge);
  • Genome-scale gene expression profiling using the Affymetrix GeneChip or Agilent DNA Microarray platforms;
  • Genome-scale screening of protein-DNA interactions, DNA copy number variations, chromosomal deletions, splicing variants, and novel transcribed sequences using Affymetrix tiling arrays, promoter arrays, and exon arrays;
  • Validation of differential gene/miRNA expression using the ABI 7900 Real-time PCR or ABI 7300 Sequence Detection qRT-PCR systems;
  • BD Antibody Protein Array Profiling;
  • Invitrogen Protein-Protein Interaction Array Hybridizations ;
  • Customized services include slide scanning, RNA extraction, RNA quality evaluation, and RNA/DNA quantification;
  • Software tutorials and microarray data analysis using Partek, dCHIP, SAM, and Ingenuity Pathway analysis software are available to all facility users; and
  • Post-experiment support in developing integrated strategies for follow-up microarray experiments.

Biomedical Research Development Facility:

  • Comprehensive mirrored genomic databases;
  • Bioinformatic software applications;
  • Custom database design; and
  • Assistance with data analysis and formulating bioinformatics sections in grant proposal and manuscripts.