Human Brain Single-cell Genomics Explorer (U24 - Clinical Trial Not Allowed)
Funding Agency:
- National Institutes of Health
Overview: Multiple consortia, both NIH and non-NIH supported, are generating large scale transcriptomic and epigenomic data at the single cell/nucleus level from human brain tissue. Efforts at the BRAIN Initiative, including BICCN and BICAN, are establishing public reference atlases of cell types in “normal” human brain, while other large-scale studies aim to query cell-type specific changes at the single cell level in disease (for example: SEA-AD, AMP-AD, AMP-PD, SCORCH, PsychENCODE). In many cases, the raw datasets being produced are accessible to only the consortium members, and the processed, clustered, and annotated data remain explorable by the public in a largely fragmented and unintegrated fashion, if at all.
Objective: The award made via this pilot program will establish an integrated resource that allows users to explore, analyze, and download processed de-identified human brain single-cell transcriptomics and epigenomics data harmonized across reference and disease datasets. Further, the recipient will provide a federated one-stop hub to access underlying raw datasets. The recipient will enlist the collaboration of at least three major existing data archives housing NIH generated datasets, ingest raw or processed data, harmonize datasets as needed, and develop a dashboard of online exploration and discovery tools. Based on the combined datasets, the recipient will create a unified cell-type taxonomy by brain region and an accompanying, community annotatable, draft cell-type nomenclature.
In addition, the recipient will work with NIH single cell consortia to develop shareable data harmonization tools, data standards, and cell type annotation and curation platforms. This effort will pilot a sustainable centralized platform for the joint analysis and exploration of NIH generated single-cell omics data, laying the groundwork for the development of community-supported human brain single-cell knowledgebases across broad disease states.
Explorer development deliverables are expected to include, but are not limited to the following portal components and functionalities:
- Single Cell Genomics Explorer will integrate all relevant dataset-specific metadata into the explorable, user-facing dataset.
- Single Cell Genomics Explorer will integrate all relevant single-cell level metadata into the explorable, user-facing dataset.
- Harmonization of datasets across datatypes and level of analysis, and provision of harmonization tools to the community.
- Minimal Explorer functionality will allow users to explore and map all cells in 2D expression/accessibility space.
- Data modalities: The Explorer functionality is to be focused on single-cell and/or single-nucleus transcriptomic or epigenomic data from human post-mortem brain tissue.
- The Explorer Knowledgebase will include a unified cell-type taxonomy and a draft, curatable cell typed nomenclature.
- Development of metrics to evaluate Explorer use by, and utility to, the community.
Additional requirements: The recipient will integrate at least three (3) major NIH-supported human single-cell omics datasets (preferably consortia generated), one of which is the combined human BICCN/BICAN human omics dataset (NEMO), while ensuring that all raw and processed data used is findable by the community.
Annual direct costs may not exceed $1M and must reflect the actual needs of the proposed project.
February 14, 2025
Daniel Miller
National Institute of Neurological Disorders and Stroke (NINDS)
Telephone: 301-496-1853
Email: daniel.miller@nih.gov
Erin E. Gray, Ph.D.
National Institute on Aging (NIA)
Telephone: 301-451-3968
Email: erin.gray@nih.gov
Deborah Henken, PhD
Eunice Kennedy Shriver National Institute of Child Health and Human Development
Telephone: 301-496-5541
Email: dh50g@nih.gov
Guoying Liu Ph.D.
National Institute of Biomedical Imaging and Bioengineering
301-594-5220
liug@mail.nih.gov
Changhai Cui, PhD
National Institute on Alcohol Abuse and Alcoholism (NIAAA)
Telephone: 301-443-1678
Email: changhai.cui@nih.gov
Emrin Horgusluoglu, Ph.D.
National Center for Complementary & Integrative Health (NCCIH)
Phone: 240-383-5302
Email: emrin.horgusluoglu-moloch@nih.gov
David Panchision, Ph.D.
National Institute of Mental Health (NIMH)
Telephone: 301-402-3969
Email: panchisiond@mail.nih.gov
Melissa Ghim, PhD
National Institute of Dental and Craniofacial Research (NIDCR)
Telephone: 301-529-6570
Email: melissa.ghim@nih.gov
Cheri Wiggs
NEI - NATIONAL EYE INSTITUTE
Phone: (301) 402-0276
E-mail: cheri.wiggs@nih.gov
John Satterlee, Ph.D.
National Institute on Drug Abuse (NIDA)
Telephone: 301-435-1020
Email:satterleej@nida.nih.gov
Jonathan Hollander, PhD
NIEHS – National Institute of Environmental Health Sciences
Phone: 984-287-3269 or 919-698-7004
Email: jonathan.hollander@nih.gov