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.

Network visualization

Latest Project Reports

Oct 2024

Tumor microenvironment in GBM

  10X Genomics Xenium by Dr. Sorana Morrissy

Sep 2024

Differential Expression Analysis

  Bulk RNA-seq by Dr. Derrick Rancourt

Aug 2024

Drug Repurposing in Breast Mets

  Nanostring GeoMx by Dr. Thomas Klonisch

Jul 2024

Endothelial Cell Markers in GBM

  10X Genomics Xenium by Dr. Janusz Rak

Jul 2024

Sarcoma Patient Case Study

  10X Genomics VisiumHD by Dr. Sorana Morrissy

 

Jun 2024

Immune Profiling in GBM Mice

  10X Genomics Xenium by Dr. Jennifer Chan

May 2024

Young Breast Cancer TME

  Nanostring GeoMx by Dr. Shirin Bonni

Apr 2024

Alzheimer's Disease Mouse Brain

  10X Genomics Xenium by Dr. Jonathan Epp

Apr 2024

Chronic Kidney Disease Biomarker

  Nanostring GeoMx by Dr. Daniel Muruve


All project reports

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Events

 

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
  6. Currently building a pipeline for the downstream/secondary analysis


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

 

Nanostring GeoMx DSP

    RunsCasesSegmentsROIsAOIs
    11 72 24 343 846

Nanostring CosMx SMI

    RunsCasesFOVsDetected cells
    1 2 289 237,972

10X Genomics Visium/Visium HD

    RunsCasesSlidesSpots
    5 16 8 2,663,032

10X Genomics Xenium In Situ

    RunsCasesFOVsDetected cells
    4 20 1,831 2,627,184
As of September 30, 2024 (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.

Pricing

Prices vary depending on cohort size, hypotheses, and expectations, which will determine the representation and interpretation. We may charge fees on an hourly or project-based basis. Please get in touch with 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

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

Oct 2024

Tumor microenvironment in GBM

  10X Genomics Xenium by Dr. Sorana Morrissy

Sep 2024

Differential Expression Analysis

  Bulk RNA-seq by Dr. Derrick Rancourt

Aug 2024

Drug Repurposing in Breast Mets

Nanostring GeoMx by
Dr. Thomas Klonisch

Jul 2024

Endothelial Cell Markers in GBM

10X Genomics Xenium by
Dr. Janusz Rak

Jul 2024

Sarcoma Patient Case Study

10X Genomics VisiumHD by
Dr. Sorana Morrissy

Jun 2024

Immune Profiling in GBM Mice

10X Genomics Xenium by
Dr. Jennifer Chan

May 2024

Young Breast Cancer TME

Nanostring GeoMx by
Dr. Shirin Bonni

Apr 2024

Alzheimer's Disease Mouse Brain

10X Genomics Xenium by
Dr. Jonathan Epp


Events

ASOC in Numbers

 

Nanostring GeoMx DSP

    RunsCasesSegmentsROIsAOIs
    11 72 24 343 846

Nanostring CosMx SMI

    RunsCasesFOVsDetected cells
    1 2 289 237,972

10X Genomics Visium/Visium HD

    RunsCasesSlidesSpots
    5 16 8 2,663,032

10X Genomics Xenium In Situ

    RunsCasesFOVsDetected cells
    4 20 1,831 2,627,184
As of September 30, 2024 (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.

Pricing

Prices vary depending on cohort size, hypotheses, and expectations, which will determine the representation and interpretation. We may charge fees on an hourly or project-based basis. Please get in touch with 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.

Certifications


 

Mailing List

Dev Environment