RNA was extracted from FACS-sorted cells at 8 distinct stages of erythropoiesis, derived from CB- and PB-CD34+ cells. cDNA libraries were prepared using the Illumina TruSeq kit and sequenced on the Illumina HiSeq 2500 (Epigenomics Core of Weill Cornell Medical College, New York). This sequencing strategy produced ~15-80 million 50bp single end reads per sample. For each distinct stage of erythropoiesis,...

Lupus nephritis is a potentially fatal autoimmune disease for which the current treatment is ineffective and often toxic. To develop mechanistic hypotheses of disease, we analyzed kidney samples from patients with lupus nephritis and from healthy control subjects using single-cell RNA sequencing. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid...

Objective: We have investigated the molecular function of SCAMP5, a candidate risk gene for SLE exclusively expressed in plasmacytoid dendritic cells (pDCs) among peripheral leucocytes. Methods: We tested the independence of the association in SCAMP5 with SLE by performing conditional analyses. We profiled the expression pattern of SCAMP5 among circulating leucocytes at the transcript and protein...

Plasmacytoid dendritic cells (pDCs) represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons (IFN-I). This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the...

In this study we sought to analyze the effects of genetic variants on gene regulation in a cell-state dependent manner during CD4 memory T cell activation. To do this, we performed an RNA-seq time series experiment on CD4 memory T cells activated with anti-CD3/CD28 beads in individuals with no autoimmune disease. We measured gene expression levels, and allele-specific expression at heterozygous sites...

Vascular smooth muscle cells (VSMCs) are key constituents of both normal arteries and atherosclerotic plaques. They have an ability to adapt to changes in the local environment by undergoing phenotypic modulation. The amino-acid glutamate has been associated with CVD risk and VSMCs metabolism in experimental vascular research, and glutamate receptors regulate VSMC biology and promote pulmonary vascular...

Here we investigated different cell populations within ovarian cancer using single-cell RNA seq: fourteen samples from nine patients with differing grades (high grade, low grade and benign) as well as different origin sites (primary and metastatic tumor site, ovarian in origin and fallopian in origin).

Using a combination of rigorous molecular genetic analyses, transgenic mice, and adoptive transfer experiments, we demonstrate that DRGs do not synthesize these antigen-specific antibodies, but rather sequester primarily IgG1 subtype antibodies. As revealed by RNA-seq and targeted quantitative PCR (qPCR), dorsal root ganglion (DRG) sensory neurons harvested from either naïve or immunized mice lack...

The cholinergic anti-inflammatory pathway (CAP), has been well-studied and shown to control peripheral cytokine levels and inflammation. This nerve pathway has been activated pharmacologically or by nerve stimulators and studied in animal models and clinical studies. However, these CAP investigations have typically been performed in models or study populations of severe systemic or pathological inflammation....

Presented is the differential expression of mRNA and miRNA in 44 Stage I and Stage II patients who developed metastasis within 5 years of nephrectomy, compared to 21 patients who remained disease free. Extracted RNA from nephrectomy specimens preserved in FFPE blocks was sequenced using RNAseq. MiRNA expression was done using the TaqMan OpenArray qPCR protocol.