HuBMAP Metadata

The metadata specifications provided here are harmonized across all versions of each specification. When uploading and ingesting data and metadata please refer to the HuBMAP Data Upload Guidelines for the latest assay metadata options and specifications and the Data Submission Guide for detailed directions on the data registraion and ingest process. See section 10 of the Guide for details on transferring metadata to the HIVE.

Donor and Sample Metadata

Dataset Metadata

The linked assay metadata pages list all attributes, as they have occurred, across any versions of the metadata specification for the given dataset type with the most current, valid set of attributes listed first on the page. The directory schema for each dataset type is also linked in the description column via the icon.

Dataset Type Description
4i 4i, or Iterative Indirect Immunofluorescence Imaging, is a high-resolution technique for imaging proteins within cells and tissues.
10X Multiome 10X Multiome is a multimodal single-cell sequencing technology that simultaneously captures both gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) from the same individual nucleus. Both RNA molecules and open-chromatin DNA fragments are labeled with a unique per-nucleus barcode using the 10x Genomics Chromium platform, allowing paired readouts to be linked to the same cell of origin.
Autofluorescence (AF) Exploits endogenous fluorescence in biological tissue to capture an image. The image can be used to integrate other images from multiple modalities and align tissues within a 3D experiment.
ATACseq Assay for Transposase-Accessible Chromatin using sequencing (ATACseq) identifies accessible DNA regions, probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome.
CODEX Co-detection by indexing (CODEX) is a strategy for generating highly multiplexed images of fluorescently-labeled antigens.
COMET COMET is a technique used to measure DNA damage in individual cells. The name comes from the shape that damaged DNA fragments form when they migrate out of a cell’s nucleus under an electric field, resembling a comet with a head and a tail. This assay is widely used in genetics research to study DNA damage from factors like radiation, chemicals, and environmental exposure.
Confocal Confocal microscopy is an advanced optical imaging technique that uses a laser and a spatial pinhole to block out-of-focus light. This method provides sharper contrast, higher optical resolution, and the ability to perform “optical sectioning” to build detailed three-dimensional images of thick specimens.
CosMx Proteomics CosMx Proteomics is a technology that enables the high-resolution, spatial analysis of proteins within their native tissue environment. It is part of the CosMx Spatial Molecular Imager (SMI) platform, which provides single-cell and subcellular resolution to map protein expression, cell states, and cell-cell interactions in FFPE and fresh frozen tissue samples.
CosMx Transcriptomics Dataset generated from performing the CosMx Transcriptomics assay.
CyCIF CyCIF, or Cyclic Immunofluorescence, is a technique used in microscopy to image multiple protein markers within a single sample. It allows for highly multiplexed immunofluorescence imaging, meaning it can detect a large number of different proteins simultaneously.
CyTOF A type of mass cytometry that employs antibodies labeled with heavy metal isotopes and uses time-of-flight mass spectrometry to analyze single cells.
DBiT-seq DBiT-seq (Deterministic Barcoding in Tissue sequencing) is a high-resolution spatial omics technology that co-maps mRNA and proteins directly on intact, formaldehyde-fixed tissue sections using a microfluidic crossflow grid. It assigns unique X-Y coordinate DNA barcodes to create a 2D mosaic of tissue “pixels” for next-generation sequencing.
DESI Desorption Electrospray Ionization (DESI), an ambient ionization technique that can be coupled to mass spectrometry (MS) for chemical analysis of samples at atmospheric conditions.
DNA Methylation DNA methylation is a critical, reversible epigenetic mechanism in biomedical research involving the addition of a methyl group to DNA (usually cytosine in CpG islands), altering gene expression without changing the underlying sequence.
Enhanced SRS Refers to improvements made to Stimulated Raman Scattering (SRS), a technique used in microscopy and spectroscopy for chemical imaging and analysis. These enhancements aim to improve sensitivity, spatial resolution, and other capabilities of SRS.
FACS FACS (Fluorescence-Activated Cell Sorting) is a specialized type of flow cytometry used to separate cells based on their unique fluorescent properties.
G4X G4X is a high-throughput spatial multiomics platform that analyzes RNA, proteins, and tissue morphology simultaneously from a single formalin-fixed paraffin-embedded (FFPE) tissue section at subcellular resolution, processing up to 128 samples per run.
GeoMx A platform for spatial biology that analyzes RNA and protein expression within tissue sections which allows for non-destructive, in situ profiling of gene expression and protein levels from specific regions of interest (ROIs) within a tissue.
HiFi Slide High-Fidelity Spatial Transcriptomic Slide (HiFi-Slide) sequencing, a super-resolution spatial transcriptomics sequencing technology, captures and spatially resolves genome-wide RNA expression in a submicron resolution for fresh-frozen tissue.
Histology The microscopic study of tissue composition and structure, often referred to as microscopic anatomy. It involves examining tissue samples, typically after they’ve been sectioned, stained, and placed under a microscope.
iCLAP iCLAP (individual-nucleotide resolution UV-crosslinking and affinity purification) is a specialized, high-stringency technique designed to map the specific RNA binding sites of RNA-binding proteins (RBPs) at the single-nucleotide level.
Illumina Spatial ver0 Illumina Spatial ver0 is a high-resolution, sequencing-based spatial transcriptomics solution that maps gene expression within intact tissue samples, preserving spatial context. It combines broad, unbiased whole-transcriptome profiling with cellular-level resolution (1-µm features) over large areas () using standard Illumina NextSeq and NovaSeq.
IMC 2D IMC 2D is two-dimensional Imaging Mass Cytometry, a specialized multiplexed single-cell proteomics and tissue-imaging technology. It combines mass spectrometry with immunohistochemistry to map the spatial distribution of dozens of protein markers across flat tissue sections.
IMC 3D 3D Imaging Mass Cytometry maps molecules and proteins inside tissues in three dimensions. It extends standard two-dimensional imaging mass cytometry by stacking multiple high-resolution scans to show cellular organization, tumor structures, and microenvironments in full 3D space.
LC-MS Coupling of liquid chromatography (LC) to mass spectrometry (MS).
Light Sheet A fluorescence imaging technique that uses a thin sheet of laser light to illuminate a sample, allowing for high-resolution, 3D imaging with reduced photobleaching and phototoxicity; particularly useful for imaging large, thick, or delicate biological samples, like developing embryos or organoids.
MACSima MACSima is a fully automated, high-content spatial biology system designed for ultra-high-plex, cyclic immunofluorescence imaging. It enables researchers to map hundreds of protein markers, and some RNAs, on a single tissue sample using MICS technology (MACSima Imaging Cyclic Staining), combining deep phenotyping with spatial context.
MALDI-IMS Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) combines the sensitivity and molecular specificity of MS with the spatial fidelity of classical microscopy.
MIBI Preserved tissue sections, mounted on conductive substrates are incubated with unique isotopic transition metal-tagged antibody reporters. An oxygen primary ion beam rasters the sample surface, ejecting and ionizing the isotope reporters. Their masses are subsequently measured via a mass analyzer.
MERFISH A spatial transcriptomics technology that allows for the simultaneous imaging of hundreds to thousands of RNA species within single cells, providing both copy number and spatial distribution information.
MPLeX MPLeX, or Metabolite, Protein, and Lipid Extraction, is a protocol for extracting and analyzing metabolites, proteins, and lipids from a single sample, and allows for comprehensive multi-omics measurements, integrating data from genomics, transcriptomics, proteomics, metabolomics, and lipidomics.
MUSIC A sequencing assay that allows profiling of gene expression, co-complexed DNA sequences, and RNA-chromatin interactions from the same single-cell nucleus. Both RNA and fragmented DNA within a nucleus are labelled with a unique cell barcode, enabling identification and matching of RNA and DNA sequences.
Paired Tag Paired-Tag (parallel analysis of individual cells for RNA expression and DNA from targeted tagmentation by sequencing) is a high-throughput, single-cell multiomics method that simultaneously maps histone modifications and gene expression (transcriptome) in the same single cell.
Pixel-seqV2 Pixel-seqV2 is a spatial transcriptomics method that utilizes polony gels to capture and sequence RNA, proteins or other molecules in tissues with high resolution. These polony gels are arrays of micron-scale DNA clusters, each containing a unique barcode, allowing for the mapping of molecules within their original spatial context in a tissue, thereby allowing researchers to study the spatial organization of cells and their gene expression profiles within tissues.
Raman-Imaging Raman Imaging is a non-invasive technique that maps the unique chemical fingerprint of biological samples (cells, tissues) by capturing Raman scattering (light interacting with molecular vibrations) at each pixel, creating detailed molecular maps showing the distribution of proteins, lipids, DNA, and water.
RNAseq While bulk RNAseq elucidates the average gene expression profile in cells comprising a tissue sample, single-cell RNAseq employs per-cell and per-molecule barcoding to enable single-cell resolution of the gene expression profile.
RNAseq with Probes Uses probes to capture and enrich specific regions of the RNA for targeted sequencing, allowing for in-depth analysis of those regions.
SHG Single-cycle Fluorescence Microscopy (SFM). A technique that utilizes the nonlinear optical phenomenon of SHG to image biological tissues and structures, particularly those containing collagen.
SeqFISH SeqFISH technology allows in situ imaging of multiple mRNAs using barcoding and fluorophore-labelled barcode readout-probes. The consortium is no longer accepting data of this type.
SIMS Secondary-ion mass spectrometry (SIMS) is a technique used to analyze the composition of solid surfaces and thin films by sputtering the surface of the specimen.
Slide-seq Provides a scalable method for obtaining spatially resolved gene expression data at resolutions comparable to the sizes of individual cells.
SnareSeq2 This method uses tagmentation within permeabilized and fixed single-nucleus isolates to capture accessible chromatin (AC) regions, followed by the capture and reverse transcription of RNA transcripts.
STARmap STARmap (Spatially-resolved Transcript Amplicon Readout Mapping) is a biomedical technology that enables the 3D mapping of gene expression within intact tissues at single-cell resolution. It combines hydrogel-tissue chemistry and in situ DNA sequencing to preserve a cell’s location and identify which genes are active in that specific spatial context. STARmap directory schema.
Stereo-seq Stereo-seq (Spatial Enhanced Resolution Omics-sequencing) is a high-resolution spatial transcriptomics technology that maps gene expression inside tissue samples. It uses DNA nanoball patterned arrays to capture RNA in situ, giving scientists a detailed look at where cells live and how they talk to each other.
Thick Section Multiphoton MxIF One version of MXIF (multiplexed fluorescence microscopy), an imaging platform whereby a large number of cellular and histological markers can be investigated on a single tissue section.
Visium HD Visium HD is a high-definition spatial transcriptomics platform that combines 2 µm resolution, gap-free oligonucleotide coverage, and the CytAssist instrument to deliver whole-transcriptome maps with single-cell precision.
Visium No Probes A spatial transcriptomics solution that allows researchers to analyze gene expression patterns within the spatial context of a tissue. An in situ method that captures RNA transcripts within the tissue and then sequences them.
Visium with Probes Offers spatially resolved transcriptomics through the 10X Genomics Visium CytAssist, which combines histology with probe-based transcriptomics in a spatial context.
WGS The process of determining the entire DNA sequence of an organism’s genome at a single time. This entails sequencing all of an organism’s chromosomal and mitochondrial DNA. The consortium is no longer accepting data of this type.
Xenium Xenium is a high-resolution, imaging-based spatial transcriptomics and spatial biology platform used to map, visualize, and quantify hundreds to thousands of RNA targets (and proteins) directly within intact tissue sections at single-cell and subcellular resolution without needing next-generation sequencing.

Other Metadata

Specification Description
Antibodies Specifics about antibodies that are used as affinity reagents in various assays.
Contributors A list of the people who contributed to the creation of a dataset. All data submitted must include a list of contributors.
Object x Analyte Standardized data matrices that represents measured analyte levels across a specific set of biological objects from associated primary data. These are Externally Processed Integrated Collections (EPICs) that have been created and submitted separately from the primary datasets
Publication A pubication page registered against the data (Datasets) that were used for the publication. See the Publication Page Submission section in the Data Submission Guide for more information on registering a publication
Segmentation Mask A digital overlay that labels and isolates specific biological structures within images submitted as part of primary datasets. These are Externally Processed Integrated Collections (EPICs) submitted separately from the primary datasets.