Services

Projects with the RIC begin with a consultation to review the scientific aims of the project and the experimental strategy, from which we will create an analysis strategy optimized for each project. This will be detailed in a project plan, prepared after the consultation, and accompanied by a timeline and quote for the initial analysis. Project plans may be updated or modified as the analysis proceeds based on feedback from researchers or the intermediate results obtained. Consultations are always free of charge. We work with data from any facility, although we encourage users to work with core facilities within the RRC.

Bioinformatics services are offered at an hourly rate of $85/hour, as well as per-unit pricing for a wide variety of standardized data processing pipelines, such as gene expression quantification from RNA-seq or taxonomic and functional profiling from shotgun metagenomics. To obtain a quote for a project, please contact us with details of your experiment so that we can determine the appropriate scope of work.

Supported analysis options include, but are not limited to:

Raw data QC and processing

• Quality control of raw FASTQ data
• Sample outlier detection
• Batch effect correction
• Genome or transcriptome alignment

Genomics

• Variant calling, annotation, and prioritization
• Genome assembly, including hybrid assemblies of long-read and short-read data sets
• Phylogenetic analysis
• Ancestry analysis

Transcriptomics

• Gene expression quantification and differential statistics
• Alternative splicing analysis
• microRNA and other small RNA expression
• Single-cell clustering and trajectory analysis

Epigenomics

• ChIP-seq and ATAC-seq peak calling and comparisons
• Bisulfite sequencing or array-based DNA methylation analysis
• Multi-omic integration, such as epigenomic and transcriptomic comparisons
• Motif analysis

Metagenomics

• Taxonomic identification and quantification for 16S amplicon sequencing
• Taxonomic and functional quantification for shotgun sequencing
• Metagenome or metatranscriptome assembly
• Diversity and differential analysis

Metabolomics

• Feature identification and quantification for metabolomics
• Differential analysis

Proteomics

• Protein identification
• Protein quantification and differential analysis in quantitative experiments

Statistics and machine learning

• Differential analysis
• Association analysis
• Clustering
• Dimensionality reduction techniques (PCA, NMDS, tSNE, UMAP)
• Supervised machine learning

Systems biology

• Pathway enrichment analysis
• Molecular interaction networks
• Biomarker discovery and comparison
• Multi-omics data integration

Data visualization

• Heatmaps, box plots, scatterplots, and other types of plots
• Genome browsers/read pileups
• Custom visualizations

The RIC provides advice and recommendations for many aspects of designing a high-throughput experiment, including:

• Next-generation sequencing versus microarray platforms
• NGS platforms (Illumina HiSeq, NextSeq, or MiSeq; PacBio or Nanopore)
• Biological replicates and sequencing depth; power recommendations
• Differences between library preparation options or microarray designs
• Batch randomization

We highly recommend scheduling a meeting with the RIC when you are in the planning stages of your experiment. There are often many options available, and the optimal one depends on your project’s aims, and is subject to limitations of sample availability and budget. These consultations are free of charge and can be arranged by contacting us. It is often also valuable to include members of the other core facilities, such as the Genomics Research Core, in these consultations.

A letter of support detailing relevant RIC resources and services, such as bioinformatics, can strengthen grant proposals. To request a letter of support or other grant support, please contact us. To help us write an effective letter of support in a timely manner, we will ask you for the following information in the request form:

• Project title
• 2-3 sentences explaining the impact of the proposed work on the scientific and/or medical community
• Specific aims (a draft is fine)
• List of experiment types and services required (e.g., RNA-seq, differential analysis and pathway analysis)
• Name of funding agency and grant type/RFA
• Deadline
• Name, title, and affiliation of addressee

In addition to Letters of Support detailing RIC capabilities as they relate to a proposed project, we can also assist with crafting the study design and research strategy, and devising a budget for informatics analysis. Please also consider including a member of the RIC as a Co-Investigator in your application, which can strengthen your application by showing the collaborative involvement and support of an informatics expert.

The RIC administers an institutional license to Ingenuity Pathway Analysis (IPA). It is used on behalf of researchers by the RIC during bioinformatics analysis and is available for researchers to use themselves.

We offer two options for UIC researchers to access IPA:

• Unlimited annual access for an annual fee of $1500/user. Users may request access to IPA through iLab at uic.edu/ipa.
• Pay-as-you-go access at an hourly rate of $100/hour, plus a one-time $50 account activation Users may request access for this option at go.uic.edu/ipa-hourly.

As part of our license, we offer a free half-day Introduction to IPA workshop once per year. In addition, users may request customized training sessions from IPA representatives at any time.

Due to the nature of our institutional license, we are only able to offer IPA access to UIC investigators. Non-UIC researchers may obtain IPA results through the RIC as part of the services provided for a project, or by obtaining their own licenses.

We teach two workshop series each year with the aim of providing researchers with practical bioinformatics skill sets to conduct bioinformatics analyses independently. Each series is five full days with a mix of hands-on exercises and lectures. Workshops are held both virtually and in person, and recordings and workshop material are made available to all registered participants. Discounted registration is available to current UIC students, sponsored by the UIC Center for Clinical and Translational Science (CCTS).

One session is held in the early summer and covers introductions to common bioinformatics topics: Introduction to R, Introduction to Linux and High Performance Computing, Introduction to RNA-seq, Introduction to Next-generation sequencing analysis, and Introduction

Metagenomics. Exercises are done in a combination of R Studio and SSH sessions on a remote high-performance compute cluster.

The second session is held in the fall and covers a variety of topics that have also proven popular: Introduction to R (same as summer), Advanced R, Advanced Statistics in edgeR, Single- cell RNA-seq, and Pathway Analysis. All of these exercises are done in R Studio.

In addition, we offer a free half-day Introduction to IPA workshop once per year. Users may also request customized training sessions from IPA field application scientists at any time.

Click here for more information on our workshops, including software requirements and setup instructions.

To stay up-to-date on current workshop offerings and other news from the RIC, please consider subscribing to our listserv: RIC_events.

The RIC has exclusive access to high-performance compute resources on the UIC Extreme supercomputer, enabling us to perform computationally-intensive analyses in a timely manner on behalf of customers. These resources include an 80-core compute queue, and a 64-core high-memory (1TB RAM) queue. We anticipate significant upgrades to these resources in the near future as UIC’s ACER group updates the computational resources on campus.