10X Genomics Spatial Gene Expression samples are now being processed on the Visium CytAssist located at the Gene Expression Center. TRIP will be assisting with the first steps of the Visium with CytAssist protocol: Histology, RNA extraction from FFPE blocks used for QC, helping to find a pathologist for ROI selection (if needed) and Visium H&E image scanning.
For Visium questions and to schedule a meeting to discuss your project and timeline, contact Gene Expression Center at: gecinfo@biotech.wisc.edu
After your meeting with GEC, please submit a TRIP iLab request.
For information on TRIP’s portion of the Visium with CytAssist collaboration with GEC.
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Information to provide TRIP for a Visium CytAssist project
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Sample Size
Each slide being run on the CytAssist will have one tissue sample centered on the slide. Based on the size of the tissue, one of two gaskets will be used. A 6.5mm x 6.5mm gasket or an 11mm x 11mm gasket.
Visium CytAssist & Visium v1 Publications
Junak M, Khatri P, Zajac J, Kubica P, Yan D, Dinh HQ, Gibson ALF. Spatial Transcriptome Analysis Reveals Diverse Human Burn Wound Microenvironment. Wound Repair Regen. 2025 Jul-Aug;33(4):e70061. doi: 10.1111/wrr.70061. PMID: 40579885; PMCID: PMC12205350.
Golfinos-Owens AE, Lozar T, Khatri P, Hu R, Harari PM, Lambert PF, Fitzpatrick MB, Dinh HQ. Integrated single-cell and spatial analysis identifies context-dependent myeloid-T cell interactions in head and neck cancer immune checkpoint blockade response. bioRxiv [Preprint]. 2025 Mar 28:2025.03.24.644582. doi: 10.1101/2025.03.24.644582. PMID: 40196610; PMCID: PMC11974738
Mohanty C, Singh CK, Daccache JA, Damsky W, Kendziorski C, Yan D, Prasad A, Zhang D, Keenan T, Drolet B, Ahmad N, Shields BE. Granuloma Annulare Exhibits Mixed Immune and Macrophage Polarization Profiles with Spatial Transcriptomics. J Invest Dermatol. 2025 Jan;145(1):109-121. doi: 10.1016/j.jid.2024.04.024. Epub 2024 Jun 4. PMID: 38844128.
Jagodinsky JC, Vera JM, Jin WJ, Shea AG, Clark PA, Sriramaneni RN, Havighurst TC, Chakravarthy I, Allawi RH, Kim K, Harari PM, Sondel PM, Newton MA, Crittenden MR, Gough MJ, Miller JR, Ong IM, Morris ZS. Intratumoral radiation dose heterogeneity augments antitumor immunity in mice and primes responses to checkpoint blockade. Sci Transl Med. 2024 Sep 18;16(765):eadk0642. doi: 10.1126/scitranslmed.adk0642. Epub 2024 Sep 18. PMID: 39292804; PMCID: PMC11522033.
Fonseca MAS, Haro M, Wright KN, Lin X, Abbasi F, Sun J, Hernandez L, Orr NL, Hong J, Choi-Kuaea Y, Maluf HM, Balzer BL, Fishburn A, Hickey R, Cass I, Goodridge HS, Truong M, Wang Y, Pisarska MD, Dinh HQ, El-Naggar A, Huntsman DG, Anglesio MS, Goodman MT, Medeiros F, Siedhoff M, Lawrenson K. Single-cell transcriptomic analysis of endometriosis. Nat Genet. 2023 Feb;55(2):255-267. doi: 10.1038/s41588-022-01254-1. Epub 2023 Jan 9. PMID: 36624343; PMCID: PMC10950360.
Ni Z, Prasad A, Chen S, Halberg RB, Arkin LM, Drolet BA, Newton MA, Kendziorski C. SpotClean adjusts for spot swapping in spatial transcriptomics data. Nat Commun. 2022 May 27;13(1):2971. doi: 10.1038/s41467-022-30587-y. PMID: 35624112; PMCID: PMC9142522.
Patil AT, Bennett DD, Xu J, Weisman P, Matson DR. Spatial transcriptomics of a giant pilomatricoma. J Cutan Pathol. 2023 Nov;50(11):963-970. doi: 10.1111/cup.14524. Epub 2023 Aug 30. PMID: 37649312; PMCID: PMC10591970.
Poster Presentations-Proffered Abstract:
Stangis, M.: Cheng, L.; Albrecht, D.; Snow, S.; Wirtz, T.; Matkowskyj, K; Dinh, D,; Kendziorski, C.; Halberg, R. Abstract 6930: Spatial analysis of multi-ancestral tumors to understand how intercellular signaling impacts tumor invasion. [abstract] In: Proceedings of the American Association for Cancer Research Annual Meeting 2024: Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl): Abstract nr 6930.
Jagodinsky JC, Vera JM, Jin WJ, Shea AG, Clark PA, Sriramaneni RN, Havighurst TC, Chakravarthy I, Allawi RH, Kim K, Harari PM, Sondel PM, Newton MA, Crittenden MR, Gough MJ, Miller JR, Ong IM, Morris ZS. Intratumoral radiation dose heterogeneity augments antitumor immunity in mice and primes responses to checkpoint blockade. Sci Transl Med. 2024 Sep 18;16(765):eadk0642. doi: 10.1126/scitranslmed.adk0642. Epub 2024 Sep 18. PMID: 39292804; PMCID: PMC11522033. (Visium v1)
