HuBMAP Data

The focus of HuBMAP is understanding the intrinsic intra-, inter-, and extra- cellular biomolecular distribution in human tissue. HuBMAP will focus on fresh, fixed, or frozen healthy human tissue using in situ and dissociative techniques that have high-spatial resolution.

The HubMAP Data Portal aims to be an open map of the human body at the cellular level. These tools and maps are openly available, to accelerate understanding of the relationships between cell and tissue organization and function and human health.

Join our mailing list to get updated on HuBMAP news, including future data releases and updates to the Data Portal.

Data Contributors

Researchers from HuBMAP Tissue Mapping Centers collected, processed and contributed tissue samples to the data portal.

Click on one of the circles to be taken to the data portal to see the datasets contributed by that group for that organ.

Expand the row for any organ to see all the assays performed on those tissues, and links to those datasets in the data portal.

CalTech TMCStanford University TMCUniversity of California San Diego TMCUniversity of Florida TMCVanderbilt University TMC
PIs Long Cai, CalTech;
Jay Shendure & Cole Trapnell, University of Washington
Mike Snyder & Garry Nolan, Stanford;
Yiing Lin, Washington University of St. Louis
Kun Zhang & Xin Sun, UCSD;
Sanjay Jain, Washington U.;
Jim Hagood, U. of North Carolina at Chapel Hill
Mark Atkinson, Harry Nick, & Kevin Otto, U. of Florida;
Bernd Bodenmiller, University of Zurich
Richard Caprioli & Jeff Spraggins, Vanderbilt
Heart
sciATAC-seq
sciATAC-seq [SnapATAC][
seqFISh
seqFISH [Lab Processed]
Kidney (left)
scATAC-seq (SNARE-seq) [Lab Processed]Autofluorescence Microscopy
SNARE-seqMALDI IMS negative
snRNA-seqMALDI IMS positive
snRNA-seq [Salmon] PAS Stained Microscopy
snRNA-seq (SNARE-seq) [Lab Processed]Untargeted LC-MS
Kidney (right)
scATAC-seq (SNARE-seq) [Lab Processed]Autofluorescence Microscopy
SNARE-seqMALDI IMS negative
snRNA-seqMALDI IMS postiive
snRNA-seq [Salmon]PAS Stained Microscopy
snRNA-seq (SNARE-seq) [Lab Processed]Untargeted LC-MS
Large intestine
Bulk ATAC-seq
Bulk ATAC-seq [BWA + MACS2]
Bulk RNA-seq
Bulk RNA-seq [Salmon]
CODEX
CODEX [Cytokit + SPRM]
snATAC-seq
snATAC-seq [Snap-ATAC]
snRNA-seq
snRNA-seq [Salmon]
Targeted Shotgun / Flow-injection LC-MS
TMT LC-MS
Untargeted LC-MS
Whole Genome Sequencing
Liver
sciATAC-seq
sciATAC-seq [SnapATAC]
Lung (right)
sciATAC-seqsnRNA-seq
sciATAC-seq [SnapATAC]snRNA-seq [Salmon]
Lymph node
CODEX
CODEX [Cytokit + SPRM]
Imaging Mass Cytometry
Lightsheet Microscopy
scRNA-seq (10x Genomics)
scRNA-seq (10x Genomics) [Salmon]
Pancreas
sciATAC-seq
sciATAC-seq [SnapATAC]
Small intestine
seqFIShBulk ATAC-seq
seqFISH [Lab Processed]Bulk ATAC-seq [BWA + MACS2]
Bulk RNA-seq
Bulk RNA-seq [Salmon]
CODEX
CODEX [Cytokit + SPRM]
Targeted Shotgun / Flow-injection LC-MS
TMT LC-MS
Untargeted LC-MS
Whole Genome Sequencing
Spleen
sciATAC-seqCODEX
sciATAC-seq [SnapATAC] CODEX [Cytokit + SPRM]
seqFISHImaging Mass Cytometry
seqFISH [Lab Processed]Lightsheet Microscopy
scRNA-seq (10x Genomics)
scRNA-seq (10x Genomics) [Salmon]
Thymus
CODEX
CODEX [Cytokit + SPRM]
Imaging Mass Cytometry
Lightsheet Microscopy
scRNA-seq (10x Genomics)
scRNA-seq (10x Genomics) [Salmon]

Explore the Data

HuBMAP-developed tools Vitessce, the Common Coordinate Framework, and Azimuth allow visual exploration of HuBMAP tissues and cells. You can also search the data in the Data Portal directly, and download data for your use.

Vitessce

Vitessce enables the exploration of spatially-resolved, integrated single-cell datasets. An interactive visualization tool, Vitessce is available for datasets that have been processed through HuBMAP HIVE computing hardware and pipelines.

The HuBMAP Mapping effort is developing a Common Coordinate Framework (CCF) for the healthy human body. This framework will support cataloging different types of individual cells, understanding the functions of and relationships between those cell types, and modeling their individual and collective function.

Elements of the CCF already in use include the ASCT+B Reporter, the Exploration User Interface, and the Registration User Interface.

The CCF ASCT+B Reporter is a visualization tool for displaying anatomical structures, cell types, and biomarkers (ASCT+B) authored by domain experts for different human organs. The tables are used to develop a Common Coordinate Framework of the healthy human body.

The CCF Exploration User Interface (EUI) supports exploration of semantically and spatially explicit data—from the whole body to the single cell level.

The CCF Registration User Interface (RUI) supports uniform tissue data registration across organs and labs.

Azimuth is a web application that uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis.

Download

While an account is not necessary to access and view datasets within the Data Portal, viewers who log in are able to download processed data.

Login to the Data Portal is handled through Globus. Login with your institutional or eRACommons credentials for anonymous access to file downloads.

About the Data

HuBMAP is transparent about the origin of its data, how the data is processed, and the quality control processes used to ensure its integrity.

HuBMAP Data comprises healthy (normal, non-diseased) tissue from over 40 donors. The data for sex, race, and ethnicity provided are those pulled from the electronic medical records available and do not reflect the breadth of human identity and experience. We hope to expand the diversity of our donors in future data releases.

Organs

Assays

HuBMAP data was generated using three modalities: mass spectrometry, microscopy, and sequencing, with a variety of assay types used in each.

Protocols

Data available through the Data Portal are linked directly to the protocols used in sample handling and assays.

Quality Control Reports

All data submitted to HuBMAP goes through a quality control process before being released to the Data Portal. Links to quality control reports are included in the Portal with the dataset information.

To stay informed about HuBMAP, including future data releases and updates to the Data Portal join our mailing list.

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Collaboration Portal