Extended Data Fig. 3: Comparing post- with pre-infusional T cell subtypes in nonCR and CR.
a, Differences in T cell subtype composition between post- and pre-infusional PBMCs from CR and nonCR. For each cell type, the log fold change in mean cell fraction between post- and pre-infusional samples was calculated with the R package speckle based on arcsin square root transformation. The cell fraction calculation includes all cell types (the denominator is the sum of all cells analyzed). For clarity, only cell types with a fold change >1.5 are shown. b, GO term enrichment analysis for DEGs comparing post- with pre-infusional PBMCs in CR and nonCR. GO terms are ranked by rich factor, which is the number of DE genes in the term divided by the number of background genes in that term. Dot plot depict the highest ranked significantly enriched GO terms for biological processes (FDR < 0.05). Cell type abbreviations: CM = central memory; EM = effector memory; TEMRA = effector memory cells re-expressing CD45RA; TPEX = precursor exhausted T cells; TEX = exhausted T cell; MAIT = Mucosal-associated invariant T cell; CTL_EOMES = eomesodermin expressing cytotoxic lymphocytes; CTL_GNLY = granulysin expressing cytotoxic lymphocytes; CTL_Exh = exhausted cytotoxic lymphocytes; Tfh T follicular helper cells; Treg = regulatory T cells; gdT = gamma delta T cell.
