Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on lipoprotein particle (LPP) exRNA profiles obtained via sequential density ultracentrifugation (SD-UC) and fast protein liquid chromatography (FPLC).
Project description:A human skin proteome MS spectral library, generated from tissue punch biopsies of the C8 paravertebral region in Parkinson's disease patients. This data and associated protocol (https://www.protocols.io/view/proteomics-sample-preparation-of-human-skin-punch-14egn9e46l5d/v1) were generated as part of a pilot study in collaboration with the Michael J. Fox Foundation. The biospecimens were obtained from the Parkinson’s Progression Marker Initiative (PPMI) (RRID:SCR_006431). For up-to-date information on the study, visit www.ppmi-info.org.
Project description:Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using novel combinations of denaturants, reducing agents, proteolysis and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and extracellular DNA (exDNA) from the same biofluid sample. We applied the method to characterize exRNAs from 312 plasma and serum samples collected from thirteen healthy volunteers at twelve time points over a two-month period.
Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To determine whether different RNA isolation kits biased detection of certain exRNA cargo types, an integrative analysis was performed using pooled plasma and serum samples, where 10 different RNA isolation kits were applied.
Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on those samples obtained via ultracentrifugation and nanoscale deterministic lateral displacement (nanoDLD).
Project description:As a core RISC component, Ago2 associates with miRNAs and target mRNAs. To identify these mRNAs, we ran lysate from HEK293T cells over a FLAG resin from 2 conditions: +FLAG-Ago2, +mock transfection. To identify mRNAs associated with specific miRNAs, we ran lysate from HEK293T cells over a FLAG resin from 2 conditions: +FLAG-Ago2 & miR-1, and +FLAG-Ago2 & miR-124. Set of arrays that are part of repeated experiments Compound Based Treatment: mock transfected Keywords: Biological Replicate
Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. In order to detect differences in density between cargo types, cushioned density gradient ultracentrifugation (C-DGUC) of serum and plasma was performed using OptiPrem (TM) density gradient.
Project description:The reduced sperm count observed in Ago2 cKO mice implies that AGO2 has non-redundant functions in the male germ line. Because AGO2 is a key protein in the RNA interference (RNAi) pathway, we first postulated that AGO2 loss disrupts normal transcriptional and translational dynamics of target mRNAs relevant to sperm maturation. To address this hypothesis, we took advantage of the apparently normal spermatogenesis in Ago2 cKO mice, which allowed us to purify matched meiotic and post-meiotic germ cells from Ago2 cKO and wild type controls. We examined changes in the transcriptome and proteome of these two spermatogenic stages in Ago2 cKO relative to control mice using RNA-seq and quantitative mass spectrometry (MS). To further examine if the changes in mRNA and protein levels detected in Ago2 cKO germ cells was due to a loss of regulation by the canonical AGO2-miRNA pathway, we characterized AGO2 protein interactors by AGO2 immunoprecipitation-mass spectrometry (IP-MS) in cytoplasmic and nuclear fractions of post-meiotic cells
