ASOC offers
Spatial Omics
Histology
Bioinformatics
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
Characterization of the GBM Mice
10X Genomics Visium by Dr. Jennifer Chan
Alzheimer’s pathogenesis in Mice
Nanostring GeoMx by Dr. Derya Sargin
Assessment of the Tx Effects
10X Genomics VisiumHD by Dr. Jennifer Chan
Profiling of the CD4+ cells
10X Genomics Xenium by Dr. Pere Santamaria
Tumor microenvironment in GBM
10X Genomics Xenium by Dr. Sorana Morrissy
Differential Expression Analysis
Bulk RNA-seq by Dr. Derrick Rancourt
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
All project reports
You'll need your authentication credentials to access the project report.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
Xenium In Situ (FFPE/FF, 250)
See the reports
Preview Data (FFPE, 5k)
See the reports
Mouse Brain (FF, 5k)
See the reports
Three Cancers (FFPE, 5k)
See the reports
Mouse Pup (FFPE, 5k)
See the reports
Human Ovary (FF, 5k)
See the reports
What's in the package?
- Analysis Summary by Xenium Ranger
- Cell-level info
- Transcripts counts
- Nucleus boundaries
- Cell X Feature matrix
- Tissue overview scan
With QC/Analysis
- Quality assessment and diagnostic plots in a Web report
- Differential expression analysis
- Cell-type deconvolution/decomposition
- Cells and target Tx visualization in regions of interest
- Publication-quality Figures upon request
ASOC in Numbers
Nanostring GeoMx DSP
| Runs | Cases | Segments | ROIs | AOIs |
|---|---|---|---|---|
| 12 | 76 | 29 | 384 | 940 |
Nanostring CosMx SMI
| Runs | Cases | FOVs | Detected cells |
|---|---|---|---|
| 1 | 2 | 289 | 237,972 |
10X Genomics Visium/Visium HD
| Runs | Cases | Slides | Spots |
|---|---|---|---|
| 7 | 16 | 11 | 4,510,975 |
10X Genomics Xenium In Situ
| Runs | Cases | FOVs | Detected cells |
|---|---|---|---|
| 11 | 34 | 3,713 | 4,969,836 |
Infrastructure
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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. Please note that we only keep backup data for up to three years due to the limited storage space.
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