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Nature | Vol 579 | 12 March 2020 | 275 tumour and NAT (Fig. 1a). To quantify our observations in these four patients, we classif ...
276 | Nature | Vol 579 | 12 March 2020 Article TCR-independent mechanisms of activation^11. In addition, subclus- ters 8.3a to 8 ...
Nature | Vol 579 | 12 March 2020 | 277 The published analysis demonstrated that new clones appear after treatment, with clonotyp ...
278 | Nature | Vol 579 | 12 March 2020 Article strength of immune response, or the ‘set point’^23 of the immune system against t ...
Methods Reagents and antibodies Antibodies used in FACS sorting were: EpCAM: Biolegend 9C4 antibody, cat. no. 324208, lot B19877 ...
Article in blood or more than one cell, respectively. To study the overlap of clonotypes between blood and tissue, we also class ...
biological processes, and ‘3.1-MT’ against the gene set for mitochondrial genes, as shown in Extended Data Fig. 4g. Comparison o ...
Article Analysis of data from Yost et al.^5 scRNA-seq counts and single-cell TCR sequences were obtained using the GEOquery libr ...
Analysis of clinical trial data Bulk tumour RNA-seq data were analysed from three clinical trials: (1) IMvigor210 (National Clin ...
Article Diedenhofen, B. & Musch, J. cocor: a comprehensive solution for the statistical comparison of correlations. PLoS On ...
Extended Data Fig. 1 | Separation of T and non-T cells. a, Criteria for separation. Clusters from the overall cluster analysis o ...
Article Extended Data Fig. 2 | Clonotype sharing and tissue expansion patterns. a, TCR sharing across compartments. Venn diagram ...
Extended Data Fig. 3 | Peripheral clonal expansion and tissue inf iltration in external dataset. The 14 patients with non-small ...
Article Extended Data Fig. 4 | See next page for caption. ...
Extended Data Fig. 4 | T cell subsets and clonal composition. a, Characterizing clusters of T cell clusters with reference gene ...
Article Extended Data Fig. 5 | See next page for caption. ...
Extended Data Fig. 5 | T cell subsets and clonal expansion behaviour. a, Tissue expansion patterns of clonotypes by T cell clust ...
Article Extended Data Fig. 6 | See next page for caption. ...
Extended Data Fig. 6 | Tissue and blood expansion patterns and T cell clusters. a, Clonal expansion scatter plots by patient. Da ...
Article Extended Data Fig. 7 | See next page for caption. ...
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