Project description:Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively. mRNA profiles of tumor and matched normal tissues from two ccRCC patients were generated by deep sequencing, using Hiseq 2000. Single-nucleotide-resolution, whole-genome, 5mC and 5hmC profiles of tumor and matched normal tissues from two ccRCC (clear cell renal cell carcinoma) patients were generated by deep sequencing, using Hiseq 2000.
Project description:The achievement of a drug-free operational tolerance for renal transplanted patients is a major goal in organ transplantation. Previous gene expression profiling in peripheral blood mononuclear cells (PBMC) identified genes associated with operational tolerance. The identification of a common pattern of B cell-related genes associated with tolerance encourage us to analyze gene expression in purified B cell from operationally tolerant patients (TOL=10) compared to renal transplanted patients with stable graft function (STA=12) under immunosuppression and also compared to healthy volunteers (HV=10) who have no immunosuppressive treatment and no graft. Microarray analyses exhibited an absence of gene signature associated with tolerance in purified B cell compared to STA or HV. These results suggest that the B cell signatures observed in PBMC may be due to an increase number of total B cells rather than specific B cell characteristics in operationally tolerant patients. This dataset represents gene expression profiling of purified B cells from 10 renal transplanted patients with operational tolerance (TOL), 12 renal transplanted patients with stable graft function under immunosuppression (STA) and 10 healthy volunteers (HV).
Project description:To further define the role of piRNAs in the development of renal cancer, we employed piRNA microarray expression profiling as a discovery platform to identify differentially expressed piRNAs. Radical nephrectomy was performed on 3 patients with renal cancer, and the postoperative pathology was clear cell renal cell carcinoma. The cancer tissues and adjacent normal tissues of the patients were taken for piRNA sequencing. And the differentially high-expressed and differentially low-expressed piRNAs were analyzed by bioinformatics.
Project description:The purpose of the study was to investigate the potential role of the immune system in renal irAEs by analyzing the features of peripheral blood mononuclear cells (PBMC) from patients with renal irAEs using single-cell RNA sequencing (scRNA-seq).
Project description:This study reports two unrelated patients with a combined immunodeficiency. Whole-exome sequencing of both patients, their healthy parents and siblings identified a single de novo missense variant in ITPR3 (NM_002224.3:c.7570C>T, p.Arg2524Cys) in both index cases. While the mRNA level in patients remained the same as in healthy siblings and controls, the level of protein expression was diminished. It was also shown that the ITPR3 heterozygous p.Arg2524Cys mutation impairs calcium flux function in dermal fibroblast of one patient and in a knock-in Jurkat T cell line. Two additional patients with related phenotypes and the same mutation were further identified and described in the study. The present dataset corresponds to the RNAseq performed on PBMC of patient 2 of the study and healthy controls.
Project description:Circulating tumor cells (CTCs) and platelets can be collected simultaneously during liquid biopsy; however, their interaction in the form of platelet-covered CTCs (pcCTCs) remains only partially understood. This submission contains single-cell RNA sequencing data generated from PBMC/buffy coat fractions from 29 donors: 12 patients with high-grade serous ovarian carcinoma, 4 non-malignant gynecological controls, 10 patients with breast cancer, and 3 healthy donor controls. The dataset was used to detect and characterize candidate naked CTCs and pcCTCs and to compare their transcriptomic profiles with platelet and cancer-related signatures.
Project description:Circulating tumor cells (CTCs) and platelets can be collected simultaneously during liquid biopsy; however, their interaction in the form of platelet-covered CTCs (pcCTCs) remains only partially understood. This submission contains single-cell RNA sequencing data generated from PBMC/buffy coat fractions from 29 donors: 12 patients with high-grade serous ovarian carcinoma, 4 non-malignant gynecological controls, 10 patients with breast cancer, and 3 healthy donor controls. The dataset was used to detect and characterize candidate naked CTCs and pcCTCs and to compare their transcriptomic profiles with platelet and cancer-related signatures.