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.

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Latest Project Reports

Jul 2025

Alzheimer’s Disease Vulnerability

  10X Genomics Xenium by Dr. Jonathan Epp

Jun 2025

Profiling Lymphatic Niches

  10X Genomics VisiumHD by Dr. Shan Liao

Jun 2025

Profiling Fetal Renal Cells

  10X Genomics Xenium by Dr. Stephane Bourque

Apr 2025

Profiling of the CD4+ cells

  10X Genomics Xenium by Dr. Pere Santamaria

Apr 2025

Profiling Gut Tissues in Rat

  10X Genomics Visium by Dr. Changting Xiao

 

Mar 2025

Heterogeneous Gastric Cancer

  10X Genomics VisiumHD by Dr. Pinaki Bose

Mar 2025

Sarcoma Patient Case Study

  10X Genomics VisiumHD by Dr. Sorana Morrissy

Feb 2025

Molecular/Physiological Changes

  Nanostring GeoMx by Dr. Jonathan Epp

Feb 2025

Transcriptomics Analysis in Muscle

  10X Genomics Xenium by Dr. Gerald Pfeffer


All project reports

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Sample QC/Analysis Reports


What's in the package?

  1. Sequencing package
  2. FASTQ files
  3. DCC files
  4. PKC file
  5. ROI report
  6. Readout package
  7. Expression profiles in EXCEL (automated)


With QC/Analysis

  1. QC report in HTML
  2. Annotation in EXCEL
  3. Diagnostic plots
  4. GeoMx objects and expression profiles after QC
  5. YAML setting file for reproducibility
  6. Analysis results, e.g., volcano plots, GO enrichment plots, etc.
  7. Publication-quality Figures upon request


What's in the package?

  1. Count matrix/Metadata in CSV
  2. Seurat object

With QC/Analysis

  1. QC, normalization, and diagnostic plots in a Web report
  2. Cell typing using InSituType
  3. Discovering modules of spatially correlated genes using InSituCor
  4. Transcripts and Cells visualization in regions of interest


What's in the package?

  1. Sequencing package
  2. BCL/FASTQ files
  3. Scan images
  4. Space Ranger report
  5. Clustering, DE analysis among clusters, tSNE results


What's in the package?

  1. Analysis Summary by Xenium Ranger
  2. Cell-level info
  3. Transcripts counts
  4. Nucleus boundaries
  5. Cell X Feature matrix
  6. Tissue overview scan


With QC/Analysis

  1. Quality assessment and diagnostic plots in a Web report
  2. Differential expression analysis
  3. Cell-type deconvolution/decomposition
  4. Cells and target Tx visualization in regions of interest
  5. Publication-quality Figures upon request

ASOC in Numbers

 

As of June 30, 2025 (update quarterly)

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. Please note that we only keep backup data for up to three years due to the limited storage space.

Publications

Impaired parvalbumin interneurons in the retrosplenial cortex as the cause of sex-dependent vulnerability in Alzheimer's disease.
Dylan J. Terstege, Yi Ren, Bo Young Ahn, Heewon Seo, Alzheimer’s Disease Neuroimaging Initiative, Liisa A. M. Galea, Derya Sargin, and Jonathan R. Epp
Sci Adv 2025;11(18):eadt8976 | DOI: 10.1126/sciadv.adt8976
Evaluating gene representation in spatial transcriptomics across pre-designed panels.
Heewon Seo and Roman Krawetz
bioRxiv 2025 | DOI: 10.1101/2025.04.07.647642

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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

Jul 2025

Alzheimer’s Disease Vulnerability

  10X Genomics Xenium by Dr. Jonathan Epp

Jun 2025

Profiling Lymphatic Niches

  10X Genomics VisiumHD by Dr. Shan Liao

Jun 2025

Profiling Fetal Renal Cells

  10X Genomics Xenium by Dr. Stephane Bourque

Apr 2025

Profiling of the CD4+ cells

  10X Genomics Xenium by Dr. Pere Santamaria

Apr 2025

Profiling Gut Tissues in Rat

  10X Genomics Visium by Dr. Changting Xiao

Mar 2025

Heterogeneous Gastric Cancer

  10X Genomics VisiumHD by Dr. Pinaki Bose

Feb 2025

Molecular/Physiological Changes

  Nanostring GeoMx by Dr. Jonathan Epp

Feb 2025

Transcriptomics Analysis in Muscle

  10X Genomics Xenium by Dr. Gerald Pfeffer


Events

News Letters

Certifications


 

Mailing List

Dev Environment