Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin (IL)-12 signaling through its downstream transcription factor STAT4 is required for the generation of memory NK cells following expansion, while type I interferon through STAT1 is important for NK cell expansion. Here, we identify gene...

Clonal expansion and immunological memory are hallmark features of the mammalian adaptive immune response and essential for prolonged host control of pathogens. Recent work demonstrated that natural killer (NK) cells of the innate immune system also exhibit these adaptive traits during infection. Here we demonstrate that differentiating and ‘memory’ NK cells possess distinct chromatin accessibility...

Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity such as clonal expansion and generation of long-lived memory. Here we look at transcriptional profiles of NK cells throughout several time points during MCMV infection, ex-vivo cytokine stimulation, and/or deficiency of key transcription factors such as STAT4, STAT1, and Runx1. In addition, we profile parallel...

Durable clinical responses to immune checkpoint inhibitors (ICB) remain limited to a minority of patients, and the molecular pathways that modulate ICB efficacy remain incompletely defined. Here we demonstrate that immunotherapy with anti-CTLA-4 and its combination with anti-PD-1 rely on melanoma cell-intrinsic activation of the cytosolic RNA receptor RIG-I. Mechanistically, tumor cell-intrinsic RIG-I...

RNA-seq performed on NK cells harvested during in-vivo infection. Natural killer (NK) cells are innate lymphocytes that have been recently appreciated to display features of adaptive immunity in response to viral infection. Biallelic mutations in the IRF8 gene have been reported to cause familial NK cell deficiency and susceptibility to severe viral infection in humans; however, the precise role...

Single-cell RNA sequencing was performed on three patients using the 10x genomics TCR profiling kits. For each patient, populations of T-cells were assayed for both TCR sequence and trancriptome-wide RNA-sequence. Two donors have a replicate experiment. From the GEO summary: "Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression...

Single-cell RNA sequencing was performed on eight donors using the InDrop v2 protocol. For each donor populations of CD45+ immune cells were assayed for trancriptome-wide RNA-sequence. At least one replicate was taken for each donor. From the GEO summary: "Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy...

Comparison of WT and GLIS3-/- cells at various stages of human pancreatic differentiation. From Gene Expression Omnibus authors' summary: "Through development and use of a minimal component protocol for derivation of late stage pancreatic progenitors and beta-like cells, we compared WT and GLIS3-/- pancreatic cells at different stages and discovered that GLIS3-/- cells show an ectopic activation...

BISCUIT (Bayesian Inference for Single-cell ClUstering and ImpuTing) provides a method for the iterative normalization and cluster of single-cell gene RNA-seq expression data. BISCUIT eases clustering of cells based on similar gene expression after correcting technical variation. The software uses a Bayesian model and employs a model driven by covariance structures for the normalization and the input...

NCBI BioProject collection containing SRA Experiment data and BioSamples resulting from "high frequency intestinal microbiota sampling in allogeneic bone marrow transplant patients, part of a larger systems biology project examining factors that influence antibiotic resistance, with a focus on the pathogens Vancomycin-Resistant Enterococcus and Klebsiella pneumoniae".