StemCore Laboratories

OVERVIEW

StemCore Laboratories is Ottawa's genomics core facility, located at the Ottawa Hospital Research Institute (OHRI) and affiliated with the University of Ottawa, serving researchers across Ottawa and beyond. 

Our cutting-edge platforms include the Illumina NovaSeq X, 10x Chromium X, and Visium HD spatial transcriptomics, supporting research from pilot projects to population-scale studies. 

With 50+ years of combined genomics expertise, we support 45+ research groups through expert consultation, state-of-the-art technology, and seamless integration with OHRI's flow cytometry and bioinformatics cores.

OUR SERVICES

AFFORDABLE SEQUENCING

Sanger sequencing and long-read plasmid verification ($6-20/sample). We also serve as Ottawa's free drop-box for Plasmidsaurus and Flow Genomics - drop off samples by Monday 10:30am for same-day shipping.

Contact: Shahriar Sheikholeslami (shsheikholeslami@ohri.ca)

SAMPLE QC/QA

Fragment Analysis, quantification and quality assessment of your samples to ensure your samples are ready for sequencing

Contact: Caroline Vergette (cvergette@ohri.ca) or Katayoun Sheikheleslamy (ksheikheleslamy@ohri.ca)

NGS (NEXT GENERATION SEQUENCING)

High-throughput sequencing on our Illumina NovaSeq X for whole genome, exome, RNA-seq, and more.

Contact: Caroline Vergette (cvergette@ohri.ca)

SINGLE CELL ANALYSIS

Uncover cellular heterogeneity with our 10x Genomics Chromium X platform for single cell RNA-seq, ATAC-seq and multi-omics. 

Contact: Katayoun Sheikheleslamy (ksheikheleslamy@ohri.ca)

POPULATION-BASED OMICS

Comprehensive bulk sequencing and multi-omics profiling including RNA-seq, proteomics (Olink), chromatin assays and methylation

Contact: Caroline Vergette (cvergette@ohri.ca)

SPATIAL BIOLOGY

Map molecular profiles within tissue architecture using Visium HD spatial transcriptomics and CellDIVE multiplexed immunofluorescent imaging.

Contact: Katayoun Sheikheleslamy (ksheikheleslamy@ohri.ca) for Visium, Damian Carragher (dcarragher@ohri.ca) for CellDIVE

ABI 3730XL Sanger Sequencing Instrument Closeup

Free Monday Drop-Box Service

We serve as Ottawa's collection point for Plasmidsaurus and Flow Genomics long-read sequencing services. 

Drop off samples by Monday 10:30am for same-day shipping at no charge. 

Drop Off Location: Sample Drop boxes are located in the CCW 5th floor lobby, which can be accessed from the Critical Care Wing Eye Institute Elevators

Questions? Contact: Damian Carragher (dcarragher@ohri.ca, ext. 73251)

SAMPLE SUBMISSION

All samples submitted to StemCore are processed through Idea Elan Infinity, our online core facility management system. Each laboratory and user must create an account before submitting samples.

To get started:

  • Visit Idea Elan Infinity.
  • Create an account with your institutional email
  • Link to your PI's funding account
  • Select your service and submit sample information

Need help? Instructions for creating accounts and submitting samples can be found in our user guides:

RECENT PUBLICATIONS


Papers, Theses and preprints that acknowledge StemCore Services

2025

Akuma, M. (2025). Characterization of Dysregulated VHL-Mediated pRb Regulation in Clear Cell Renal Cell Carcinoma [PhD Thesis, Université d’Ottawa/University of Ottawa]. 

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Clémot-Dupont, S., Lourenço Fernandes, J. A., Larrigan, S., Sun, X., Medisetti, S., Stanley, R., El Hankouri, Z., Joshi, S. V., Picketts, D. J., Shekhar, K., & Mattar, P. (2025). The chromatin remodeler ADNP regulates neurodevelopmental disorder risk genes and neocortical neurogenesis. Proceedings of the National Academy of Sciences, 122(3), e2405981122. 

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Cober, N. D., McCourt, E., Godoy, R. S., Deng, Y., Schlosser, K., Qamsari, E. S., Azami, J., Salehisiavashani, E., Cook, D. P., & Lemay, S.-E. (2025). Mapping disease-specific vascular cell populations responsible for obliterative arterial remodelling during the development of pulmonary arterial hypertension. Cardiovascular Research, 121(13), 2095–2112. 

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Esper, M. E., Lin, A. Y., Bennett, D., & Rudnicki, M. A. (2025). Intrinsic dysfunction in muscle stem cells lacking dystrophin begins during secondary myogenesis. Nature Communications, 16(1), 10031. 

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Jahan, S., Maganti, H. B., Patel, J., Pasha, R., Doxtator, E., Manesia, J. K., & Pineault, N. (2025). Reduction in cord blood graft potency due to processing delay can be prevented by trehalose supplementation. Vox Sanguinis, vox.70012. 

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Jo, D.-H. (2025). Innovative Approaches to Natural Killer Cell Engineering: Overcoming Challenges in CRISPR-Cas9 Genome Editing, Transgene Expression, and Cryopreservation [PhD Thesis, Université d’Ottawa/University of Ottawa]. 

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Jo, D.-H., Kaczmarek, S., Khan, A. U. H., Pervin, J., Clark, D. M., Gadde, S., Wang, L., McComb, S., Visram, A., & Lee, S.-H. (2025). Entinostat, a histone deacetylase inhibitor, enhances CAR-NK cell anti-tumor activity by sustaining CAR expression. Frontiers in Immunology, 16, 1533044. 

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Larrivée, M. (2025). Generating CAR γδ T Cells for Effective Targeting of B Lymphomas [PhD Thesis, Université d’Ottawa| University of Ottawa]. 

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Losier, T. T., King, K. E., Rousseaux, M. W., & Russell, R. C. (2025). Identification of organelle-specific autophagy regulators from tandem CRISPR screens. Journal of Cell Biology, 224(10), e202405138.

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Martell, E., Kuzmychova, H., Senthil, H., Chawla, U., Kaul, E., Grewal, A., Banerji, V., Anderson, C. M., Venugopal, C., & Miller, D. (2025). Disease stage-specific role of the mitochondrial pyruvate carrier suppresses differentiation in temozolomide and radiation-treated glioblastoma. Neuro-Oncology, noaf008. 

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Noblett, N. (2025). Exploring the Role for IPPK-1 and PAL-1 in the Genetic Landscape of C. elegans Ventral Nerve Cord Assembly [PhD Thesis, Université d’Ottawa| University of Ottawa]. 

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Noblett, N., Roenspies, T., Flibotte, S., & Colavita, A. (2025). Nuclear hormone receptor regulation of Caudal mediates ventral nerve cord assembly in C. elegans. bioRxiv

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Parweez, F., Palou, R., Li, R., Kadhim, L., MacMillan, H., Tyers, M., & Johné Liu, X. (2025). Engineered spermidine-secreting Saccharomyces boulardii enhances olfactory memory in Drosophila melanogaster. bioRxiv

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Shah, S., Lourenço Fernandes, J. A., Medisetti, S., & Mattar, P. (2025). Chd4 remodels chromatin to control retinal cell type specification and lineage termination. bioRxiv

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Zuccarini, R. (2025). The Effect of Sox9 on Cell Growth and Stemness in HER2-Positive Breast Cancer [PhD Thesis, Université d’Ottawa/University of Ottawa]. 

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2024

Angka, L., Tennakoon, G., Cook, D. P., Martel, A. B., Market, M., de Souza, C. T., Cummins, E., Samudio, I., Kekre, N., & Ardolino, M. (2024). Preventing surgery induced immune suppression and metastases by inhibiting PI3K-gamma signalling in Myeloid-Derived Suppressor Cells. bioRxiv

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Bergin, C. J., Zouggar, A., Mendes da Silva, A., Fenouil, T., Haebe, J. R., Masibag, A. N., Agrawal, G., Shah, M. S., Sandouka, T., Tiberi, M., Auer, R. C., Ardolino, M., & Benoit, Y. D. (2024). The dopamine transporter antagonist vanoxerine inhibits G9a and suppresses cancer stem cell functions in colon tumors. Nature Cancer

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Bhattarai, K. R. (2024). Deciphering the Role of ARK5 and hnRNP A1 in Regulating the Osmotic Stress. [PhD Thesis, Carleton University].

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Clemot-Dupont, S., Fernandes, J. A. L., Larrigan, S., Sun, X., Medisetti, S., Stanley, R., El Hankouri, Z., Joshi, S. V., Picketts, D. J., & Shekhar, K. (2024). The ChAHP chromatin remodelling complex regulates neurodevelopmental disorder risk genes to scale the production of neocortical layers. bioRxiv

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Cyr-Depauw, C., Cook, D. P., Mižik, I., Lesage, F., Vadivel, A., Renesme, L., Deng, Y., Zhong, S., Bardin, P., Xu, L., Möbius, M. A., Marzahn, J., Freund, D., Stewart, D. J., Vanderhyden, B. C., Rüdiger, M., & Thébaud, B. (2024). Single-Cell RNA Sequencing Reveals Repair Features of Human Umbilical Cord Mesenchymal Stromal Cells. American Journal of Respiratory and Critical Care Medicine.

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Gatica, D., Alsaadi, R. M., El Hamra, R., Mueller, R., Miyazaki, M., Sad, S., & Russell, R. (2024). The ER-phagy receptor FAM134B is targeted by Salmonella Typhimurium to promote infection. bioRxiv

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Kalinina, A. (2024). The Differential Regulation of Adult Neural Stem Cells by Beclin1 and Atg5 [PhD Thesis, Université d’Ottawa/University of Ottawa]. 

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Kalinina, A., Dhaliwal, J., Xue, Y., Vaculik, M., McCambley, M., Fong, B. C., Cook, D., Slack, R. S., & Lagace, D. C. (2024). Mitotic Activity and DNA Maintenance of Adult Neural Stem Cells is Regulated by Beclin1. bioRxiv

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Kornfeld, S. F., Cummings, S. E., Yaworski, R., De Repentigny, Y., Gagnon, S., Zandee, S., Fathi, S., Prat, A., & Kothary, R. (2024). Loss of miR-145 promotes remyelination and functional recovery in a model of chronic central demyelination. Communications Biology, 7(1), 813. 

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Leung, J. W.-H., Loan, A., Xu, Y., Yang, G., Wang, J., & Chan, H. M. (2024). Reduction of Glyoxalase 1 Expression Links Fetal Methylmercury Exposure to Autism Spectrum Disorder Pathogenesis. Toxics, 12(7), Article 7. 

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Li, J., Vranjkovic, A., Read, D., Delaney, S. P., Stanford, W. L., Cooper, C. L., & Crawley, A. M. (2024). Lasting differential gene expression of circulating CD8 T cells in chronic HCV infection with cirrhosis identifies a role for Hedgehog signaling in cellular hyperfunction. Frontiers in Immunology, 15.

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Loan, A., Awaja, N., Lui, M., Syal, C., Sun, Y., Sarma, S. N., Chona, R., Johnston, W. B., Cordova, A., & Saraf, D. (2024). Single-cell profiling of brain pericyte heterogeneity following ischemic stroke unveils distinct pericyte subtype-targeted neural reprogramming potential and its underlying mechanisms. Theranostics, 14(16), 6110. 

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Losier, T. T., Rousseaux, M. W., & Russell, R. C. (2024). Identification of stress specific autophagy regulators from tandem CRISPR screens. bioRxiv

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Molyer Yildirir, B. (2024). SMAC Mimetics Sensitize HIV-Infected Cells to MG1-Mediated Death [PhD Thesis, Université d’Ottawa | University of Ottawa]. 

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Peneycad, C. J. (2024). The splicing inhibitor isoginkgetin induces transcription of metallothionein genes through the metal responsive transcription factor MTF-1 [PhD Thesis, Carleton University]. 

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ProProwse, N. (2024). The Truncated Tropomyosin Kinase B Receptor Influences Feeding Behaviour, Cholesterol Production and Susceptibility to Stress in a Sex-Dependent Manner [PhD Thesis, Carleton University]. 

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Prykhozhij, S. V., Ban, K., Brown, Z. L., Kobar, K., Wajnberg, G., Fuller, C., Chacko, S., Lacroix, J., Crapoulet, N., & Midgen, C. (2024). miR-34a is a tumor suppressor in zebrafish and its expression levels impact metabolism, hematopoiesis and DNA damage. PLoS Genetics, 20(5), e1011290. 

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Rodriguez, G. M., Yakubovich, E., Maranda, V., Hanna, A. M. R., & Vanderhyden, B. C. (2024). NLRC5 overexpression in ovarian tumors remodels the tumor microenvironment and increases T-cell reactivity toward autologous tumor-associated antigens. Frontiers in Immunology, 14

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Russell, R., Akuma, M., Kim, M., Zhu, C., Wiljer, E., Gaudreau-Lapierre, A., Patterson, L., Trinkle-Mulcahy, L., Stanford, W. L., & Riazalhosseini, Y. (2024). Loss of VHL-mediated pRb regulation promotes clear cell renal cell carcinoma. bioRxiv

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Suk, T. R., Part, C. E., Nguyen, T. T., Zhang, J. L., Heer, M. M., Caballero-Gomez, A., Grybas, V. S., McKeever, P. M., Nguyen, B., & Callaghan, S. M. (2024). A stress-dependent TDP-43 SUMOylation program preserves neuronal function. bioRxiv

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CONTACT US

Damian Carragher, PhD - Director, StemCore Laboratories

(613) 737-8899 ext 73251

dcarragher@ohri.ca

Critical Care Wing 5132, 

Ottawa Hospital Research Institute, 

501 Smyth Rd.

Ottawa

ON, K1H 8L6

Kathy Sheikheleslamy - Single Cell and Spatial Biology Specialist

(613) 737-8899 x73251

ksheikheleslamy@ohri.ca

Critical Care Wing 5132, 

Ottawa Hospital Research Institute, 

501 Smyth Rd.

Ottawa

ON, K1H 8L6

Caroline Vergette - NGS Specialist

(613) 737-8899 x73251

cvergette@ohri.ca

Critical Care Wing 5132, 

Ottawa Hospital Research Institute, 

501 Smyth Rd.

Ottawa

ON, K1H 8L6

Shahriar Sheikholeslami - Affordable Sequencing Specialist (Long Read and Sanger)

(613) 737-8899 x73629

shsheikholeslami@ohri.ca

Critical Care Wing 5132, 

Ottawa Hospital Research Institute, 

501 Smyth Rd.

Ottawa

ON, K1H 8L6