NeMO Archive — Neuroscience Multi-Omic Archive

Overview

The NeMO Archive (Neuroscience Multi-Omic Archive) is a data repository for multi-omic single-cell data from the NIH BRAIN Initiative and the primary archive for BICAN (BRAIN Initiative Cell Atlas Network) datasets. Hosted at the University of Maryland Institute for Genome Sciences, NeMO stores and distributes single-cell and single-nucleus sequencing data from human, non-human primate, and mouse brain studies. As of April 2025, NeMO Archive was removed from the Recherche Data Gouv list of trusted thematic repositories. The France perspective covers the background.

What NeMO Stores

NeMO stores scRNA-seq and snRNA-seq (single-cell and single-nucleus transcriptomics of brain tissue) as AnnData/h5ad files. It also stores scATAC-seq (chromatin accessibility), spatial transcriptomics (MERFISH, Slide-seq, Visium), multi-omics (joint transcriptome and chromatin accessibility), epigenomics (DNA methylation), and processed data including cell type annotations and clustering results.

Access Model

NeMO operates a tiered access model. Processed data (cell type annotations, metadata, summary files) is freely downloadable without registration. Raw data from human subjects requires a data access request managed through the NeMO Access portal, similar to dbGaP. The NeMO Analytics workspace provides cloud-based analysis of controlled-access data without requiring download.

BICAN Datasets

NeMO is the primary repository for BICAN data. The Human Brain Cell Atlas provides a comprehensive human brain single-cell taxonomy covering millions of cells across all major brain regions. Non-human primate atlases cover macaque and marmoset brain cell types. The mouse brain atlas continues and expands BICCN mouse data. Spatial transcriptomics datasets include MERFISH brain maps with cell type spatial distributions.

Data Standards

• Primary data format is AnnData / h5ad for processed data.
• Raw reads in FASTQ format are deposited in NCBI SRA, cross-linked from NeMO records.
• Cell type annotations use Cell Ontology (CL) terms.
• Anatomy annotations use UBERON brain region terms.
• Data transfer is supported via REST API and AWS S3.

Connections

• Part of: NIH BRAIN Initiative / BICAN

Resources

• https://nemoarchive.org
• https://assets.nemoarchive.org (NeMO Analytics workspace)
• https://nemoarchive.org/data-access-request (controlled access request)