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.

Donors

HuBMAP Data comprises healthy (normal, non-diseased) tissue from over 30 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

The initial data release for HuBMAP encompasses over 300 data sets spanning seven organ types: heart, kidney, large intestine, small intestine, lymph nodes, spleen and thymus. Specimen types (fresh frozen tissue section, FFPE, single cell cryopreserved, etc.) are associated with the organs and can be used to filter during exploration.

Additional organs will be part of future releases.

Assays

HuBMAP data was generated through three modalities: mass spectrometry, microscopy, and sequencing, with a variety of assay types used in each. This table shows which assays were applied to each organ type.

Search the Data

Anyone can access the Data Portal without login and browse, download metadata, and visualize public data.

The Data Portal allows users to browse by Donors, Samples, Datasets, and Collections. Viewers can refine their search by organ type, specimen type, assay type, donor information, group (who produced the data), and more.

Explore the Data

HuBMAP team members are developing tools to allow visual exploration of HuBMAP tissues and cells.

Common Coordinate Framework

One of the goals for the Consortium is to develop a reference map or coordinate system that will incorporate multiple datatypes to detail specific tissue regions.

For the initial HuBMAP data release, kidney and spleen tissue sample locations are mapped three-dimensionally against a human reference image.

Links to view the datasets are available for further exploration in the visualization map.

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.

Download the Data

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 institution credentials for anonymous access to file downloads.

Protocols

Samples available through the Data Portal have direct links to the protocols for sample handling and assays.

Metadata

Associated metadata is also included to provide additional insight on the tissue health and how the samples were handled prior to acquisition.

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.

Data Contributors

Researchers from HuBMAP Tissue Mapping Centers collected, processed and contributed the tissue samples. This table shows which tissues were contributed by each group.

PI & Institution Heart Kidney Large intestine Lymph nodes Small intestine Spleen Thymus
Long Cai, CalTech;
Jay Shendure & Cole Trapnell, University of Washington
sciATACseq seqFISH seqFISH
sciRNAseq
seqFISH
Mike Snyder & Garry Nolan, Stanford University;
Yiing Lin, Washington University of St. Louis
ATACseq (bulk) ATACseq (bulk)
CODEX CODEX
RNAseq (bulk) RNAseq (bulk)
snATACseq Shotgun LC-MS (targeted)
snRNAseq TMT LC-MS
Shotgun LC-MS (targeted) Untargeted LC-MS
TMT LC-MS WGS
Untargeted LC-MS
WGS
Kun Zhang & Xin Sun, University of California San Diego;
Sanjay Jain, Washington University;
Jim Hagood, University of North Carolina at Chapel Hill
SNAREseq2
Mark Atkinson, Harry Nick, & Kevin Otto, University of Florida;
Bernd Bodenmiller, University of Zurich
CODEX CODEX CODEX
IMC IMC IMC
scRNAseq (10XGenomics) scRNAseq (10XGenomics) scRNAseq (10xGenomics)
Richard Caprioli & Jeff Spraggins, Vanderbilt University AF
Antibody-based MxIF
MALDI negative
MALDI positive
PAS
Shotgun LC-MS (proteomics)
Collaboration Portal