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Bioinformatics services offered by the CRI cover a wide range of computational molecular biology applications, including genomics (DNA sequence variation), transcriptomics (gene expression), epigenomics (gene regulation), and metagenomics (microbiome). We provide services covering a wide variety of technologies, including:

  • Quality control of raw FASTQ data
  • Genome or transcriptome alignment
  • Variant calling and annotation for genome resequencing projects
  • Gene or transcript quantification and differential analysis for RNA-seq
  • ChIP-seq peak calling and comparison
  • Metagenomics and metatranscriptomics analysis
  • Quality control and normalization steps for microarray expression data
  • Quality control and genotyping for Affymetrix Gene Titan arrays
  • Quality control and normalization options for single-cell sequencing or qPCR studies
  • Integration with proteomics and metabolomics data

We also offer collaborative, custom analysis solutions for any research project, and encourage researchers to consider collaborating with the CRI for all analysis stages of a project. Such projects could include integration of multiple types of -omics data, such as ChIP-seq and RNA-seq; systems biology applications such as network and pathway analysis; and the creation of customized pipelines for researchers. We work with data from any facility, although we have a close relationship with UIC DNA services (DNAS) and the Core Genomics Facility (CGF), which provide excellent options for data collection at UIC.

In addition to support for any of the above types of analysis, the CRI also advises on experimental design, helping researchers optimize their use of biological replicates and sequencing depth; provides services like study design and randomization; creates custom visualizations of data, such as heat maps; and helps with manuscript preparation and grant applications.