The NanoFlow Repository

Abstract

Motivation Extracellular particles (EPs) are the focus of a rapidly growing area of exploration due to the widespread interest in understanding their roles in health and disease. However, despite the general need for EP data sharing and established community standards for data reporting, no standard repository for EP Flow cytometry (EP-FC) data captures rigor and minimum reporting standards such as those defined by MIFlowCyt-EV (Welsh et al., 2020)[https://doi.org/10.1080/20013078.2020.1713526]. We sought to address this unmet need by developing the NanoFlow Repository. Results We have developed The NanoFlow Repository to provide the first implementation of the MIFlowCyt-EV framework. Availability: The NanoFlow Repository is freely available and accessible online at https://genboree.org/nano-ui/. Public datasets can be explored and downloaded at https://genboree.org/nano-ui/ld/datasets. The NanoFlow Repository’s backend is built using the Genboree software stack that powers the ClinGen Resource, specifically the Linked Data Hub (LDH), a REST API framework written in Node.js, developed initially to aggregate data within ClinGen (https://ldh.clinicalgenome.org/ldh/ui/about). NanoFlow’s LDH (NanoAPI) is available at https://genboree.org/nano-api/srvc. NanoAPI is supported by a Node.js Genboree authentication and authorization service (GbAuth), a graph database called ArangoDB, and an Apache Pulsar message queue (NanoMQ) to manage data inflows into NanoAPI. The website for NanoFlow Repository is built with Vue.js and Node.js (NanoUI) and supports all major browsers. Supplementary information Supplementary data are available at Bioinformatics online.

Toward a human brain extracellular vesicle atlas: Characteristics of extracellular vesicles from different brain regions, including small RNA and protein profiles

“…We have submitted all relevant data of our experiments to the EV‐TRACK knowledgebase (EV‐TRACK ID: EV230055). 31 Reporting for NFCM was submitted to the NanoFlow Repository 32 and can be accessed via https://genboree.org/nano‐ui/team/1760529291 based on reporting standards defined by MIFlowCyt‐EV framework. 33 Nucleic acid sequencing data were deposited with the Gene Expression Omnibus, accession GSE226490.…”