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Genomics Core Facility

The Saint Louis University Genomics Core Facility offers a range of services to both internal and external users. The goal of the Core is to make genomics-based projects easy and accessible to all researchers regardless of their experience with genome wide research.

The Genomics Core houses a 10X Genomics Chromium Controller which has the capability for single cell RNA-sequencing, single cell immune profiling, and single nuclear Assay for Transposase Accessible Chromatin (ATAC) sequencing experiments.

Sequencing is also offered for standard bulk RNA and Chromatin Immunoprecipitation (ChIP) which are sequenced in house on the Ion Torrent Proton Sequencing System. We can also apply our sequencing technology to specialized applications, such as mutation identification and targeted sequencing.

In collaboration with the Saint Louis University Research Microscopy and Histology Core, we also offer full services for Digital Spatial Profiling experiments for both transcriptomics and proteomics performed on the Nanostring GeoMx Digital Spatial Profiling platform.

The core can assist users on all aspects of their genome-wide experiments from experimental design through custom data analysis. Additionally, users can seek bioinformatic assistance with projects obtained through an external sequencing provider or assistance with sample preparation for submission to external sequencing providers.

Available Services

Single Cell Sequencing Technologies

Single cell sequencing can address tissue specific and/or cell type specific biological questions by examining RNA expression on the single cell level.

The core facility can provide library preparation and data analysis services for a number of 10X Genomics platform single cell technologies including 3’ and 5’ RNA-seq, Single Cell Immune Profiling, and ATAC (Assay for Transposase Accessible Chromatin) -seq.

Digital Spatial Profiling

Digital spatial profiling can answer key biological questions related to tissue heterogeneity through molecular profiling.

Through a collaboration with the Saint Louis University Research Microscopy and Histology Core, we can provide library preparation and data analysis services for Nanostring GeoMx Digital Spatial Transcriptomic and Proteomic profiling of tissue samples.

Genome-Wide RNA Transcript Analysis

Many biological questions can be addressed by determining the genome-wide patterns of gene expression by measuring RNA levels.

The core facility can provide services including RNA isolation and data analysis, for Ion TorrentTM Proton nextgen sequencing approaches to quantify mRNAs, non-coding RNAs, and small RNAs such as microRNAs. For most total RNA sequencing experiments, we require 1 ug of total RNA, though. Less may be required depending on the application.

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. These data can provide insights into gene regulatory pathways and epigenetic control of gene expression.

In general, the facility does not prepare chromatin or perform the immunoprecipitation, but can provide suggested protocols and advice for these experiments. In some cases, a collaboration for chromatin preparation and immunoprecipitation may be established. Starting from input and precipitated chromatin, the facility can use Ion TorrentTM 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 TorrentTM 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.

Amplicon Sequencing

The Ion Torrent ProtonTM 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.

Custom Projects

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. We also welcome Ion Torrent compatible libraries for direct-to-sequencing services.

Nucleic Acid Quality Analysis

The core facility uses a QubitTM fluorimeter to quantify small amounts of RNA and DNA. Detailed analysis of size distribution, quantity, and quality is performed using an AgilentTM bioanalyzer. Quality analysis can be provided as a service independent from nextgen sequencing for a nominal cost.

Bioinformatic Analysis

Basic data analysis is included in the cost of most sequencing services we offer. Additional in-depth analysis is available at an hourly rate. We can also provide bioinformatic support for projects sequenced outside of the core.

How to Start a Project

All projects are initiated by consultation with Michelle Pherson to design protocols that address the project in an efficient and cost-effective manner. There is no charge for consultation – just ask!

For sample submission, please download and fill out our Sample Intake Form. Bring a completed copy with your samples or email the completed form to Michelle.

Michelle Pherson, Ph.D.
Research Lab Supervisor
Doisy Research Center, Room 439
314-977-9252
michelle.pherson@health.slu.edu

Project Pricing

An important goal of the Genomics Core Facility is to make genomic methods both affordable and timely for SLU researchers. All charges are thus based on time and materials (sequencing chips, reagents, etc.). Sequencing uses the Ion Torrent ProtonTM, which can complete runs within two days and does not require multiple simultaneous projects for time-effective operation.

View or download the current pricing schedule for full details. An example project pricing sheet is available as well.