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: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:We investigated the gene expression of the human TM. We isolated TM cells from healthy human donor eyes. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.
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:Circulating extracellular RNAs (exRNAs) have great promise as novel clinically plasma-based biomarkers for cancer diagnosis and prognosis. knowledge of the difference or association between these different sources of exRNAs is very limited. We performed a sequential physical and biochemical precipitation to receive 4 plasma fractions (platelets and cell debris, Thrombin-treated fraction, extracellular vesicles and supernatant) from each plasma sample. After total RNA extraction, we made ligation-free libraries and performed RNA-seq to evaluate full spectrum of RNA abundance in each fraction. All RNAs were included without size selection during the library preparation. We utilized a successive stepwise alignment strategy to map the RNA sequences to different RNA categories. We found that each plasma fraction had its own unique distribution of RNA species. Hierarchical cluster analysis showed similarity in samples with same fraction and significant differences between different fractions. In addition, we also observed abundance difference of unique transcript. Furthermore, a considerable proportion of exogenous RNAs and novel predicted miRNAs in all plasma fractions were detected. These results demonstrate that thorough inspection of all plasma fractions is necessary for exRNA-based biomarker study and appropriate sampling processes is needed for illustrating the complexity of plasma-based EVs study.
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).