Extended Data Fig. 6: Spatial transcriptomics (ST) data processing and the association between eFibro_CTHRC1 and immune infiltration.
Related to Fig. 4. (a) Workflow of ST data collection and processing, including quality control and identification of malignant cells, clustering, and annotation. (b) A representation of Hematoxylin and eosin (H&E) stained tissue sections from a patient’s ST spot, along with spatial feature plots detailing read counts and feature numbers for a single ST spot. H&E image reproduced with permission from ref. 39, AAAS. Scale bars, 50 μm. (c) Spatial feature plot identifying malignant cells as predicted by CopyKat. (d) Spatial feature plot depicting the deconvolution output from STRIDE. (e) Spatial feature plot demonstrating the results of clustering analysis. (f) Violin plot showing the CTHRC1+ fibroblasts signature score across different spatial clusters. (g) Box plots illustrating the inferred associations between inducers of CTHRC1+ fibroblasts and their signature scores. The red box represents data calculated from 62 ST samples, while the green box is derived from 9,460 samples across 23 cancer types in the TCGA project. The bottom of each box indicates the Q1, and the top represents the Q3. The height of the box reflects the IQR, and the horizontal line inside the box indicates the median. The whiskers extend to the positions of Q1 - 1.5 * IQR and Q3 + 1.5 * IQR. (h) Comparative box plots of CD8 + T cell infiltration levels in 9,460 samples from the TCGA project, comparing high and low CTHRC1+ fibroblast signature scores, stratified by cancer type, as estimated by Cibersort. The bottom of each box indicates the Q1, and the top represents the Q3. The height of the box reflects the IQR, and the horizontal line inside the box indicates the median. The whiskers extend to the positions of Q1 - 1.5 * IQR and Q3 + 1.5 * IQR. (i) Box plots comparing the CD8+ T cell infiltration in 9,460 samples from the TCGA project with high versus low CTHRC1+ fibroblasts signature score across different cancer types, with estimations based on EPIC. The bottom of each box indicates the Q1, and the top represents the Q3. The height of the box reflects the IQR, and the horizontal line inside the box indicates the median. The whiskers extend to the positions of Q1 - 1.5 * IQR and Q3 + 1.5 * IQR.
