Overview

The Bioinformatics Shared Resource continuously develops new and efficient approaches to data analysis as a response to emerging research needs. Facility functions include: statistical analyses and computational modeling; advanced bioinformatics tools for integrative cancer biology; and data management. Routine data analyses include large scale information datasets (omics data) generated by high-throughput technologies, which address the following areas:

Services

• Gene expression (bulk RNA-seq including single-cell RNA-seq both regular and spatial, smRNA-seq, Nanostring, legacy microarrays)
• Gene regulation (ChIP-seq, CUT&RUN, ATAC-seq, epigenetic profiling, methylation assays)
• 3D genome organization (HiC, Hi-ChIP)
• Genome and transcriptome sequencing (alternate splicing, RNA editing, mutation detection, CNV)
• Biomarkers (discovering markers in mRNA, miRNA and protein expression data)
• Proteomic analyses (mass spectrometry-based spectra, LCMS, DIGE, RPPA, etc.)
• Polymorphism genotyping (e.g. Single Nucleotide [SNP] and Copy Number variations [CGH], LOH)
• Pathway and network analysis
• Integration of multi-platform data
• Other customized data analysis projects

Services

• High-throughput data analysis:
  • Next generation sequencing data analysis
  • Single cell RNA-seq
  • Hybridization platforms (Nanostring, microarrays)
  • Low-density PCR arrays (mi-RNA, pathways, custom)
  • Proteomics and metabolomics data
  • Enrichment Analysis (Ingenuity, DAVID)
• Comprehensive analysis of complex projects that require multi-platform data integration
• Consultation and support of experimental design and customized bioinformatics services
• Statistical consultation and predictive model building
• Computational support for data management, high performance computing, and custom programming
• Centralized computation resources, including data management and collaboration tools, sequence databases, homology algorithms, and other sequence manipulation tools
• Web-based application/database development and management
• Training: Genome Browser, Ingenuity, DAVID
• Grant and publication support: results, methods, figures
• Advanced biological models and illustrations

Equipment and Features

• High-performance computational clusters
• Integrated Wizko IT infrastructure
• Dedicated servers
• Access to storage and backup

Pricing

For pricing information, visit iLab or contact the managing director.

This facility is supported in part by a Cancer Center Support Grant (CCSG) awarded by the National Cancer Institute (NCI) to the Ellen and Ronald Caplan Cancer Center.