HuBMAP Metadata by Dataset Type

A list of available dataset types (data types from multiple supported assays), with a link to the valid metadata attributes for each dataset type. 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.

Dataset Type	Description
4i	4i, or Iterative Indirect Immunofluorescence Imaging, is a high-resolution technique for imaging proteins within cells and tissues.
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. Link to AF directory schema.
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. Link to ATACsec directory schema.
CODEX	Co-detection by indexing (CODEX) is a strategy for generating highly multiplexed images of fluorescently-labeled antigens. Link to CODEX directory schema.
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.
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.
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. Link to DESI directory schema.
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. Link to Enhanced SRS directory schema.
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. Link to GeoMx directory schema.
HiFi	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. Link to HiFi directory schema.
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. Link to Histology directory schema.
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	Combines standard immunohistochemistry with CyTOF mass cytometry to resolve the cellular localization of up to 40 proteins in a tissue sample. Link to IMC directory schema.
LC-MS	Coupling of liquid chromatography (LC) to mass spectrometry (MS). Link to LC-MS directory schema.
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. Link to Light Sheet directory schema.
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. Link to MALDI-IMS directory schema.
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. Link to MIBI directory schema.
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. Link to MERFISH directory schema.
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. Link to MUSIC directory schema.
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. Link to TSM MxIF directory schema.
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.
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. Link to RNAseq directory schema.
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. Link to RNAseq with Probes directory schema.
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. Link to Raman Imaging directory schema.
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. Link to SHG directory schema.
SeqFISH	SeqFISH technology allows in situ imaging of multiple mRNAs using barcoding and fluorophore-labelled barcode readout-probes. Link to SeqFISH directory schema. 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. Link to SIMS directory schema.
Slide-seq	Provides a scalable method for obtaining spatially resolved gene expression data at resolutions comparable to the sizes of individual cells. Link to Slide-seq directory schema.
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. Link to SnareSeq2 directory schema.
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.
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. Link to Visium NP directory schema.
Visium with Probes	Offers spatially resolved transcriptomics through the 10X Genomics Visium CytAssist, which combines histology with probe-based transcriptomics in a spatial context. Link to Visium with Probes directory schema.
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. Link to WGS directory schema. The consortium is no longer accepting data of this type.