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Physically Isolated OptiPrep (TM) Fractions for exRNA Analysis

ABSTRACT: Physically Isolated OptiPrep (TM) Fractions for exRNA Analysis

PROVIDER: PRJNA510087 | ENA |

REPOSITORIES: ENA

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Physically Isolated OptiPrep (TM) Fractions for exRNA Analysis

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.

2018-12-15 | GSE123864 | GEO

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Project description:All cells secrete extracellular RNA (exRNA), however the roles of secreted RNAs are still not fully understood. Here, we are profiling the small RNAs secreted from Caco-2 cells. ExRNAs were isolated as different fractions: total extracellular, intravesicular, extravesicular, and nonvesicular (abitrarily named as Total ExRNA P40, P100, S100).

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Two distinct extracellular protein signatures released by a single cell type identified by LC-MS/MS

Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

2018-10-26 | PXD004931 | Pride

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