The Genomics Core Facility enables Saint Louis University investigators to use whole genome methods in their research. Our services use high-throughput nextgen DNA sequencing with the Ion Torrent Proton™ platform from Life Technologies.
Services include genome-wide RNA expression analysis (RNA-seq), genomic chromatin immunoprecipitation using nextgen sequencing (ChIP-seq), and whole mammalian exome and small genome sequencing. We can also apply the technologies to specialized applications, such as mutation identification and targeted sequencing. Assistance with data analysis is also provided.
Genome-Wide RNA Transcript Analysis
Many biological questions can be addressed by determining the genome-wide patterns of gene expression by measuring RNA levels. SLU’s Genomics Core Facility can provide services including RNA isolation and data analysis, for Ion Torrent™ Proton nextgen sequencing approaches to quantify mRNAs, non-coding RNAs and small RNAs such as microRNAs. Depending on the method used, we can start with as little as 50 ng of total RNA.
Genome-Wide Chromatin Immunoprecipitation
Chromatin immunoprecipitation is used to determine where specific proteins bind chromosomes and the locations of histone modifications and other epigenetic marks. This data can provide insights into gene regulatory pathways and epigenetic control of gene expression.
The facility does not prepare chromatin or perform the immunoprecipitation but can provide suggested protocols and advice for these experiments. Starting from input and precipitated chromatin, the facility can use Ion Torrent™ sequencing to quantify binding or chromatin mark enrichment genome-wide.
Exome and Small Genome Sequencing
Genetic variations in coding sequences of mammalian and smaller genomes can be discovered by sequencing all known exons and comparing to reference sequences. The Ion Torrent™ also has the capacity to sequence entire small genomes for comparison to a reference genome. We can generate sequences of small genomes for organisms that have not previously been sequenced, but we currently do not provide genome assembly services.
The Ion Torrent Proton™ sequencing technology is well-suited to sequencing specific sets of genes or other features, such as all known oncogenes, starting with as little as 10 ng of genomic DNA. This feature is useful for re-sequencing of particular gene sets of interest. Life Technologies has many pre-designed amplicon libraries, and custom amplicon libraries can also be designed using web-based tools.
In addition to standard nextgen sequencing services (RNA-seq, ChIP-seq, exome, genome and amplicon sequencing), custom sequencing protocols can be designed, such as sequencing of selected oligonucleotide libraries. We can also design protocols for measuring nascent RNA and run-on transcription approaches.
Nucleic Acid Quality Analysis
The core facility uses a Qubit™ fluorometer to quantify small amounts of RNA and DNA. Detailed analysis of size distribution, quantity and quality is performed using an Agilent bioanalyzer. Quality analysis can be provided as a service independent from nextgen sequencing for a nominal cost.
The core facility has installed Partek™ software to facilitate analysis of nextgen sequence data, including gene ontology and pathway analysis. Partek™ provides a graphical user interface that makes it easy for users to conduct their own analysis but the core facility can also conduct the analysis for users. There is an hourly charge for the use of the Partek™ software to cover the cost of the yearly license. Ion Reporter™ software uses cloud computing to detect genetic variations, such as SNPs, insertions, deletions and CNVs in genome sequence data.
How to Start a Project
All projects are initiated by consultation with Michelle Pherson, Ph.D., to design protocols that address the project in an efficient and cost-effective manner. There is no charge for a consultation.
Michelle Pherson, Ph.D.
Research Lab Supervisor
Doisy Research Center, Room 439
The Genomics Core Facility aims to make genomic methods both affordable and timely for SLU researchers. All charges are based on time and materials (microarrays, sequencing chips and reagents).
Sequencing uses the Ion Torrent Proton, which can complete runs within two days and does not require multiple simultaneous projects for cost-effective operation.
Contact Michelle Pherson to discuss your proposed project and obtain a detailed cost estimate and a projected timeline for completion. The quote will include all materials, labor costs, equipment usage fees and software licensing. Cost comparisons for different approaches can also be provided.
As an example, a typical mammalian genome-wide RNA transcript quantification experiment with three control and three experimental replicates (six total samples) will cost between $3,000 and $3,500, depending on whether or not you isolate the RNA or do your own bioinformatic analysis.