Project description:The development of single cell transcriptomic technologies yields large datasets comprising multimodal informations such as transcriptomes and immunophenotypes. Currently however, there is no software to easily and simultaneously analyze both types of data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes of functional maturation in peripheral T lymphocytes from healthy donors. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.
Project description:Blood samples were collected from healthy volunteers, PBMC were collected using standard ficoll centrifugation. RNA was collected from untreated and PBMC treated with 15 µM L-sulforaphane for 24 hours. Libraries were prepared for mRNA-Seq.
Project description:IL-2 mutant (F42K) is a variant of IL-2 that binds preferentially to the lower affinity IL-2Rβγ and has minimal binding to CD25, on Tregs, effector NK and T-cell subsets. Our recent study has uncovered that in contrast to WT IL-2, F42K did not efficiently induce the expansion of highly suppressive ICOS+ Tregs in PBMC from healthy controls and melanoma patients whereas it did promote the expansion of NK cells. We used microarray to study the differences of gene profiles induced by wild-type (WT) IL-2, F42K and IL-15 when treated on freshly isolated human peripheral blood mononuclear cells (PBMC) from healthy control.
Project description:Whole blood was collected from healthy and autistic infants and peripheral blood mononuclear cells (PBMC) were isolated. Transcriptional profile in PBMCs was compared between healthy and autistic infants.
Project description:IL-2 mutant (F42K) is a variant of IL-2 that binds preferentially to the lower affinity IL-2Rβγ and has minimal binding to CD25, on Tregs, effector NK and T-cell subsets. Our recent study has uncovered that in contrast to WT IL-2, F42K did not efficiently induce the expansion of highly suppressive ICOS+ Tregs in PBMC from healthy controls and melanoma patients whereas it did promote the expansion of NK cells. We used microarray to study the differences of gene profiles induced by wild-type (WT) IL-2, F42K and IL-15 when treated on freshly isolated human peripheral blood mononuclear cells (PBMC) from healthy control. Human peripheral blood mononuclear cells (PBMC) were isolated from buffy coat and were stimulated with 0.4nM WT IL-2, F42K or IL-15 for 24 hr. Total RNA was extracted from each WT IL-2, F42K and IL-15 treated PBMCs and Sense RNA was reverse-transcribed via RT reaction into DNA and labeled with biotin using Affymetrix labeling kits and hybridized on human Affymetrix microarray chip.
Project description:Multiple myeloma (MM), also known as plasma cell myeloma, is a cancer of plasma cells, a type of white blood cell normally responsible for producing antibodies. There is no cure for MM. In addition, the mechanism underlying abnormal production of plasma cells is not clear. In this experiment, peripheral blood was obtained from normal healthy donors and multiple myeloma (MM) patients. Peripheral blood mononuclear cells (PBMC) were separated by Ficoll separation solution. Samples of four donors were pooled and Samples of four MM patients were pooled. The aim was to characterize the mRNA profile of MM patients compared to healthy donors and find the new target of diagnosis or treatment for MM.
Project description:Systemic lupus erythematosus (SLE), also known simply as lupus, is an autoimmune disease. There is no cure for SLE. The mechanism involves an immune response by autoantibodies against a person's own tissues. However, the mechanism underlying imbalance of autoantibodies is not clear. In this experiment, peripheral blood was obtained from normal healthy donors and systemic lupus erythematosus (SLE) patients. Peripheral blood mononuclear cells (PBMC) were separated by Ficoll separation solution. Samples of four (total eight) donors were pooled and Samples of four (total eight) SLE patients were pooled. The aim was to characterize the mRNA profile of SLE patients compared to healthy donors and find the new target of diagnosis or treatment for SLE.
Project description:This study examines circulating PBMC miRNAs of adult human subjects before and after bovine milk intake. We sought to confirm and expand findings previously reported by Baier, et al., J Nutr, 2014, PMID 25122645, using the same samples. PBMC RNA samples were provided by the Zempleni lab (see Baier, et al., J Nutr, 2014, PMID 25122645) and had been taken from five healthy donors prior to milk intake (T0) and at six hours post-intake (T6). miRNA profiles were generated for each sample by OpenArray (Thermo Fisher).
Project description:The goal of this study was to characterize altered inducible immune networks in Systemic onset juvenile idiopathic arthritis (sJIA), an IL-1-driven autoinflammatory disease of unknown etiology. To this end, we developed a high-throughput assay that quantifies the transcriptional and protein-level responses of blood leukocytes to innate stimuli. Herein, we report transcriptional data from healthy adult blood stimulated with 16 different conditions, including TLR ligands, cytosolic receptor ligands and inflammatory cytokines. We further report blood transcriptional profiles from sJIA patients with various disease activity and treatment statuses, both ex vivo (baseline) and after in vitro stimulation with a subset of innate stimuli including heat-killed bacterial pathogens.