Spatial Omics Bioinformatics and Beyond
Novel Technology in Spatial Omics and Bioinformatics Analysis
Spatial Transcriptomics and Proteomics
The Applied Spatial Omics Centre (ASOC) at the Cumming School of Medicine, University of Calgary, in response to the rapid growth and increasing demand in the field of spatial High-Plex Technology, is offering an essential development for our research landscape: Spatial Transcriptomics and Proteomics Analysis Service. This endeavour signifies a strategic response to an evolving necessity within biological research - the need for high-resolution spatial context in studying gene and protein expression.
Why Work with Us
Expertise
- Specialized team dedicated to support
- Transparency and open communication
- End-to-end service
Adaptability
- Diverse services for all tech needs
- Customizable options and rates
- Open to faculty and external clients
Affordability
- Services at cost (non-profit)
- Centralization ensures top-tier equipment access
Service Workflow
Project initiation and experimental design
- Project review
- Platform and service overview
- Sample discussion
- ROI selection strategy
- Timeline & costs
Quality control and histology service
- Histology instruction and consultation
- Optimizing immunofluorescence morphology markers
- Tissue process, if required
Spatial biology platform run and high-throughput sequencing
- Slide preparation
- Platform operation
- Readouts
- Post-staining
Bioinformatics data analysis and visualization
- QC and raw data preprocessing
- Expression normalization
- Deconvolution/enrichment test
- Support visualization
- Data export and backup
Design Considerations for Spatial Omics Experiments
The contents in this section were adopted from Williams et al. (PMID: 35761361) and please read the paper for more information.
What is my experimental aim?
A. Hypothesis generating?
B. Hypothesis testing?
(See below for more information)
Can I use spatial transcriptomics?
I. Does my tissue need optimization?
II. Is there enough RNA in the sample?
III. Are my targets detectable?
IV. Are large numbers of replicates needed?
| A. Hypothesis Generating | B. Hypothesis Testing | |
|---|---|---|
| Target | Many genes | Few genes |
| Resolution | 2-1000 cells / spot | single-cell |
| Area | Large | Small |
| Comment | Available for Xenografts | Determine cell types with specific markers |
| Platforms | GeoMx or Visium CytAssist | CosMx or Xenium In Situ |
Bioinformatics Analysis
ASOC Bioinformatics team aims to accelerate Spatial Omics research and its applications in clinical practice and provide customized and case-by-case analysis services for the life science research community. Their mission is to develop the bioinformatics capacities at the CSM (Cumming School of Medicine) to ensure that researchers derive maximum benefits from Spatial Omics data.
Due to the limited capacity, Bioinformatics Analysis is available for those who run Spatial Omics platforms within the Centre and they have a priority. With Spatial Omics data, we offer an (integrative) analysis of the genomic, bulk/single-cell transcriptomic, and pharmacological profiles as well as well-characterized public datasets.
All services include a report, a set of codes to reproduce, publication-quality Figures upon request, and a storage (backup) to store raw data, processed data, reports, and code for one year. If you’d like to keep the data for over a year, let us know as soon as possible.
Our services:
- Semi-automated QC report
- Basic analysis
- Semi-automated QC report
- Normalization and outlier detection, i.e., principal component analysis (PCA)
- Differential Expression (DE) analysis: statistical testing results and volcano plots
- Gene-set enrichment test or Hypergeometric test
- Subsequent analysis within a month
- Advanced analysis
- Basic analysis
- Feature selection, i.e., highly variable genes
- Sample (hierarchical) clustering using features: heat map with clinical annotation
- Cell-type deconvolution
- Integrative analysis
- Advanced analysis
- Include in-house/public data, e.g., bulk RNA-seq, in the analysis pipeline
- Raw data processing, e.g., STAR alignment (2-PASS), quantification, etc.
- Subsequent analysis within two months
- One-on-one spatial data analysis workshop
- Help to set up analysis environment, i.e., R and Docker
- Finger exercise and replicate the QC report
- Bioinformatics counseling for subsequent analysis and validation methods
Beyond these analysis services, contact us to discuss further. We will provide data analysis of the sequence-level genomes and transcriptomes, pharmacological profiles, drug combination effects, and CRISPR screens on top of the Spatial Omics profiles.
Pricing
Prices vary depending on cohort size, hypotheses, and expectations, which will determine the representation and interpretation. We may charge fees on an hourly basis or a project base. Please contact us for further inquiries.
We currently have very limited IT infrastructure support from the Research Computing Services at the University of Calgary. If you'd like to boost your project in a timely manner, we can fulfill services using Amazon Web Services (Cloud) at your expense. On the other hand, we can offer services at a reduced price when our Bioinformatics team can access your resources where we can store your data. If you have an account on Advanced Research Computing, we can work more seamlessly. Thank you very much for your consideration.