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. 2023 Nov 16;14:7432. doi: 10.1038/s41467-023-43201-6

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Illustration of the workflow combining spatially resolved transcriptomics with T cell receptor profiling in the SPTCR-seq protocol. Independent from the standard Visium protocol, the yield of 100 ng full-length cDNA is taken to enrich TCR transcripts through hybridization. After long-read sequencing on the nanopore platform, intensive postprocessing is applied and data will be integrated through the R-based software tool SPATAImmune. b H&E histological image of the sample UKF313 with annotation of defined histological regions. Surface plots indicate the abundance of TCR chains. c Scatter plot of TRA UMI counts per spot (y-axis) and TRB UMI counts per spot (y-axis). Pearson correlation R = 0.693, p < 2.2 × 10⁻¹⁶. d Surface plot of the single-cell composition after deconvolution with CytoSPACE22. Surface plot of the T cell abundance using Cell2Location scores (e) or the expression of TRBC2 (f). Surface plots contain the dimensions of the samples (in mm) on the x and y axes. Partially created with BioRender.com.