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Cell–cell communications of various cell populations within tumor microenvironment play an essential role in primary tumor growth, metastasis evolution, and immune escape. Nevertheless, comprehensive investigation of cell–cell communications in the ccR
Combining bulk and single-cell TCR-seq datasets, we evaluated if the expanded clones post-treatment (1) displayed cluster structure; (2) if clustered clones were drug-bound; and (3) if clustered, drug-bound clones were novel or pre-existing. We constructed cluster networks for ADR013 and AD...
et al. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief. Bioinform. 22(6). (2021). Papalexi, E. & Satija, R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat. Rev. Immunol. 18(1), 35–45 (2018). Article...
(P50-CA101942-12), DOD CDMRP (W81XWH-18-1-0480), and in part by Bristol-Myers Squibb. D.A.B. is supported by the John. R. Svenson Fellowship. C.J.W. acknowledges support from NIH: NCI-1RO1CA155010 and NIH/NCI U24 CA224331. This work was supported in part by The G. ...
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To analyze differential expressed genes between sample fractions for the same cell type (for example metastatic tumor cells vs. primary tumor cells), pseudo-bulk differential expression analysis [17] was applied by aggregating the counts of a group of cells from the same individual. We used estima...
Additionally, IM3 tumors had increased CD8+T cell infiltration. The proportion of terminal exhausted T cells was also higher in IM3 tumors, followed by IM4 tumors, which was confirmed by bulk-seq data (Extended Data Fig.4a,b). Substantial differences were observed in TAMs of IM3 and IM4 tu...
the traditions of the early scribes and printers and carvers have decayed, we have become so used to inferior forms and arrangements that we hardly realize how poor the bulk of modern lettering really is. In the "revival" of printing and book decoration, many attempts have been made to ...
Our study suggests that CD72 is associated with tumor immunity and may be a biomarker relevant to the diagnosis and prognosis of KIRC patients. Introduction Renal cell carcinoma (RCC) is one of the ten most common cancers; 73,750 new cases of RCC and 14,830 RCC deaths were reported in th...