Figure S3.

Hi-C data characterization and GSEA of T_CM and T_EM signature genes. (A) Correlation heatmap showing reproducibility of Hi-C libraries from T_N and T_EFF cells. Pearson correlation coefficient between Hi-C library pairs was determined using ChrInt scores at 10 kb resolution as the input data (see details in Materials and methods). (B) Diagram illustrating the summation approach underlying the Hi-C pile-up profile centered on specific genomic locations (sites of interest). The ChrInt between the regions flanking the sites of interest is aggregated in section A, while that within the region on either side of the sites is in sections C. The interaction of the sites with its flanking regions is projected on lines B. (C–F) RNA-seq data on T_CM and T_EM cells were retrieved and processed in-house. By requiring ≥1.5-fold changes, FDR < 0.05, and fragments per kilobase of exon per million mapped fragments at the higher expression condition ≥1, we identified 144 genes as T_CM signature and 231 genes as T_EM signature genes. The enrichment of these signature genes in WT and Ctcf^−/− early T_EFF transcriptomes was determined with GSEA. (C and D) T_CM signature is enriched in Ctcf^−/− early T_EFF cells, with 49 T_CM signature genes in the leading edge. C, enrichment plot; D, heatmaps of the top 40 genes in the leading edge, with genes of interest in red font. (E and F) T_EM signature is enriched in WT early T_EFF cells, with 44 T_EM signature genes in the leading edge. E, enrichment plot; F, heatmaps of the top 40 genes in the leading edge, with genes of interest in red font. Marked in enrichment plot are NES (normalized enrichment score), NOM P val (nominal P values), and FDR q-val (FDR q values) as output from GSEA. Note that similar results were obtained with T_CM and T_EM signature gene sets defined in GSE147080 (Millner et al., 2020).