ASOC offers
Spatial Omics
Bioinformatics
and Beyond
The Applied Spatial Omics Centre (ASOC) constitutes the hub of Spatial Transcriptomics/Proteomics and Bioinformatics. ASOC provides advanced genomic technologies and cutting-edge methods to researchers and clinicians at the University of Calgary as well as external academic and industry Scientists.
Latest Project Reports
Drug Repurposing in Breast Mets
Nanostring GeoMx by Dr. Thomas Klonisch
Endothelial Cell Markers in GBM
10X Genomics Xenium by Dr. Janusz Rak
Sarcoma Patient Case Study
10X Genomics VisiumHD by Dr. Sorana Morrissy
Immune Profiling in GBM Mice
10X Genomics Xenium by Dr. Jennifer Chan
Young Breast Cancer TME
Nanostring GeoMx by Dr. Shirin Bonni
Chronic Kidney Disease Biomarker
Nanostring GeoMx by Dr. Daniel Muruve
Alzheimer's Disease Mouse Brain
10X Genomics Xenium by Dr. Jonathan Epp
Spatial Profiling in Mouse Spleen
10X Genomics Xenium by Dr. Pere Santamaria
Sarcoma Patient Case Study
10X Genomics Visium by Dr. Franz Zemp
All project reports
You'll need your authentication credentials to access the project report.Events
Sample QC/Analysis Reports
Spatial Organ Atlas, Brain
See the report
Brain Tissue Markers
See the ROIs
Spatial Organ Atlas, Kidney
See the report
Kidney Tissue Markers
See the ROIs
Spatial Organ Atlas, Liver
See the report
Liver Tissue Markers
See the ROIs
What's in the package?
- Sequencing package
- FASTQ files
- DCC files
- PKC file
- ROI report
- Readout package
- Expression profiles in EXCEL (automated)
With QC/Analysis
- QC report in HTML
- Annotation in EXCEL
- Diagnostic plots
- GeoMx objects and expression profiles after QC
- YAML setting file for reproducibility
- Analysis results, e.g., volcano plots, GO enrichment plots, etc.
- Publication-quality Figures upon request
Tonsil
(1000-plex)
Frontal Cortex (6,278-plex)
See the reports
Pancreas (18,946-plex)
See the reports
What's in the package?
- Count matrix/Metadata in CSV
- Seurat object
With QC/Analysis
- QC, normalization, and diagnostic plots in a Web report
- Cell typing using InSituType
- Discovering modules of spatially correlated genes using InSituCor
- Transcripts and Cells visualization in regions of interest
What's in the package?
- Sequencing package
- BCL/FASTQ files
- Scan images
- Space Ranger report
- Clustering, DE analysis among clusters, tSNE results Currently building a pipeline for the downstream/secondary analysis
Human Liver Non-deseased
See the reports
Human Breast Cancer
See the reports
Mouse Brain Replicate 1
See the reports
What's in the package?
- Count matrices and metadata
- Xenium Ranger report
With QC/Analysis
- QC, normalization, and diagnostic plots in a Web report
- DE analysis and functional annotation
- Cell-type deconvolution
- Transcripts and Cells visualization in regions of interest
ASOC in Numbers
Nanostring GeoMx DSP
| Runs | Cases | Segments | ROIs | AOIs |
|---|---|---|---|---|
| 11 | 72 | 24 | 343 | 846 |
Nanostring CosMx SMI
| Runs | Cases | FOVs | Detected cells |
|---|---|---|---|
| 1 | 2 | 289 | 237,972 |
10X Genomics Visium/Visium HD
| Runs | Cases | Slides | Spots |
|---|---|---|---|
| 5 | 16 | 8 | 2,663,032 |
10X Genomics Xenium In Situ
| Runs | Cases | FOVs | Detected cells |
|---|---|---|---|
| 4 | 20 | 1,831 | 2,627,184 |
Infrastructure
 |
We have a few different strategies for backing up your data, as ARC (Advanced Research Computing) does not perform backups, and for recovering from disasters. We implemented a common backup rule, the 3-2-1 backup rule, which states that we should have three copies of data stored on at least two different types of media, one of which should be offsite. At ASOC, raw data is triplicated: (1) It remains in the instruments/internal storage, (2) We will copy it to the ARC storage, and (3) We will sync it to the offsite backup storage. We also triplicate the final products: (1) Web servers where users can directly access their reports, (2) The second snapshot is stored in the local computer/cloud storage where the final products were generated, and (3) The offsite backup storage.
In sum, we periodically back up both raw data and final products to the offsite backup storage. On the other hand, processed data, which can be generated again, will eventually be removed elsewhere.
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 ARC, we can work more seamlessly. Thank you very much for your consideration.
Certifications
Mailing List
Dev Environment
