diff --git a/docs/assays/metadata/4i-(Iterative-Indirect-Immunofluorescence-Imaging).md b/docs/assays/metadata/4i.md similarity index 100% rename from docs/assays/metadata/4i-(Iterative-Indirect-Immunofluorescence-Imaging).md rename to docs/assays/metadata/4i.md diff --git a/docs/assays/metadata/HiFi-Slide.md b/docs/assays/metadata/HiFi.md similarity index 99% rename from docs/assays/metadata/HiFi-Slide.md rename to docs/assays/metadata/HiFi.md index 52c63d6..ca89eb5 100644 --- a/docs/assays/metadata/HiFi-Slide.md +++ b/docs/assays/metadata/HiFi.md @@ -1,7 +1,7 @@ --- layout: page --- -# HiFi-Slide +# HiFi
Version 2 (current) diff --git a/docs/assays/metadata/SecondHarmonicGeneration.md b/docs/assays/metadata/SecondHarmonicGeneration.md index bf2cd76..22b4169 100644 --- a/docs/assays/metadata/SecondHarmonicGeneration.md +++ b/docs/assays/metadata/SecondHarmonicGeneration.md @@ -1,7 +1,7 @@ --- layout: page --- -# Second-Harmonic-Generation +# SGH
Version 2 (current) ## Version 2 (current) diff --git a/docs/assays/metadata/ThickSectionMultiphotonMxIF.md b/docs/assays/metadata/ThickSectionMultiphotonMxIF.md index 90ebb39..a623824 100644 --- a/docs/assays/metadata/ThickSectionMultiphotonMxIF.md +++ b/docs/assays/metadata/ThickSectionMultiphotonMxIF.md @@ -1,7 +1,7 @@ --- layout: page --- -# Thick-Section-Multiphoton-MxIF +# MxIF
Version 2 (current) ## Version 2 (current) diff --git a/docs/assays/metadata/index.md b/docs/assays/metadata/index.md index 973d251..db8c27f 100644 --- a/docs/assays/metadata/index.md +++ b/docs/assays/metadata/index.md @@ -1,49 +1,47 @@ --- layout: page --- -## HuBMAP Metadata Attributes by Dataset Type +## HuBMAP Metadata by Dataset Type -This is a list of available dataset types (data types from multiple supported assays), with links to the valid metadata attributes for each dataset type. The linked assay 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. +A list of available dataset types (data types from multiple supported assays), with a link [](EnhancedSRS "Attribute description") 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. -| Datsaset Type | Attributes | Description | -|-------|------------|-------------| -| 4i (Iterative Indirect Immunofluorescence Imaging) | [attributes](4i-(Iterative-Indirect-Immunofluorescence-Imaging)) | 4i, or Iterative Indirect Immunofluorescence Imaging, is a high-resolution technique for imaging proteins within cells and tissues. | -| [Autofluorescence](https://docs.hubmapconsortium.org/assays/af) | [attributes](AutoFluorescence) | Exploits endogenous fluorescence in a biological tissue to capture an image. The image can then be used to integrate other images from multiple modalities and to align tissues within a 3D experiment. | -| [ATACseq](https://docs.hubmapconsortium.org/assays/atacseq)| [attributes](ATACseq) | Identifies accessible DNA regions by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. | -| [CODEX](https://docs.hubmapconsortium.org/assays/codex) | [attributes](CODEX) | Strategy for generating highly multiplexed images of fluorescently-labeled antigens. | -| COMET | [attributes](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 | [attributes](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. | -| CyCIF | [attributes](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 | [attributes](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. | -| DESI | [attributes](DESI) | | -| Enhanced SRS | [attributes](EnhancedSRS) | | -| FACS | [attributes](FACS) | FACS (Fluorescence-Activated Cell Sorting) is a specialized type of flow cytometry used to separate cells based on their unique fluorescent properties. | -| GeoMx | [attributes](GeoMx) | | -| HiFi | [attributes](HiFi-Slide) | | -| Histology | [attributes](Histology) | | -| [IMC](https://docs.hubmapconsortium.org/assays/imc) | [attributes](IMC) |Combines standard immunohistochemistry with CyTOF mass cytometry to resolve the cellular localization of up to 40 proteins in a tissue sample. | -| [LC-MS](https://docs.hubmapconsortium.org/assays/lcms) | [attributes](LC-MS) | Coupling of liquid chromatography (LC) to mass spectrometry (MS) | -| iCLAP | [attributes](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. | -| Light Sheet | [attributes](LightSheet) | | -| [MALDI-IMS](https://docs.hubmapconsortium.org/assays/maldi-ims) | [attributes](MALDI) | 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. | -| MERFISH | [attributes](MERFISH) | | -| MIBI | [attributes](MIBI) | | -| MPLEx | [attributes](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 | [attributes](MUSIC) | | -| Olink | [attributes](Olink) | Olink utilizes Proseek reagents based on PEA, a Proximity Extension Assay technology, to allow 96 oligonucleotide-labeled antibody pairs to bind to their respective protein targets in the sample. A PCR reporter sequence is formed by a proximity-dependent DNA polymerization event and is subsequently detected and quantified using real-time PCR. | -| [RNAseq](https://docs.hubmapconsortium.org/assays/rnaseq) | [attributes](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.| -| Pixel-seqV2 | [attributes](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 | [attributes](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 With Probes | [attributes](RNAseqWithProbes) | | -| Second Harmonic Generation | [attributes](SecondHarmonicGeneration) | | -| Seq-Scope | [attributes](Seq-Scope) | Seq-Scope is a spatial barcoding technology that enables high-resolution, unbiased spatial transcriptomics analysis by repurposing the Illumina sequencing platform, thereby allowing researchers to visualize gene expression at a cellular and subcellular level. | -| [SeqFISH](https://docs.hubmapconsortium.org/assays/seqfish) | [attributes](seqFISH) | seqFISH technology allows in situ imaging of multiple mRNAs using barcoding and fluorophore-labelled barcode readout-probes. | -| SIMS | [attributes](SIMS) | | -| Slide-seq | [attributes](Slide-seq) | | -| SnareSeq2 | [attributes](SnareSeq2) | | -| STARmap | [attributes](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. | -| Thick Section Multiphoton MxIF | [attributes](ThickSectionMultiphotonMxIF) | | -| Visium HD | [attributes](Visium-HD) | Visium HD is a high-resolution, whole-transcriptome spatial transcriptomics platform that maps gene expression with near-single-cell resolution across an intact tissue section, unlike traditional methods that lose spatial context through tissue dissociation. | -| Visium No Probes | [attributes](VisiumNoProbes) | | -| Visium With Probes | [attributes](VisiumWithProbes) | | -| WGS | [attributes](WGS) | | + +| Dataset Type | Description | +|--------------|-------------| +| [4i](https://hubmapconsortium.github.io/ingest-validation-tools/4i/current/) [](4i "Attribute description")| 4i, or Iterative Indirect Immunofluorescence Imaging, is a high-resolution technique for imaging proteins within cells and tissues. | +| [Autofluorescence (AF)](https://docs.hubmapconsortium.org/assays/af) [](AutoFluorescence "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/af/current/). | +| [ATACseq](https://docs.hubmapconsortium.org/assays/atacseq) [](ATACseq "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/atacseq/current/). | +| [CODEX](https://docs.hubmapconsortium.org/assays/codex) [](CODEX "Attribute description")| Co-detection by indexing (CODEX) is a strategy for generating highly multiplexed images of fluorescently-labeled antigens. Link to [CODEX directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/codex/current/). | +| COMET [](COMET "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/cosmx-proteomics/current/) [](CosMx Proteomics "Attribute description")| 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. | +| [DESI](https://pmc.ncbi.nlm.nih.gov/articles/PMC6053038/) [](DESI "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/desi/current/). | +| [Enhanced SRS](https://www.nature.com/articles/s41467-019-13230-1) [](EnhancedSRS "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/enhanced-srs/current/). | +| [GeoMx](https://nanostring.com/products/geomx-digital-spatial-profiler/spatial-multiomics-enabled-with-geomx-dsp/) [](GeoMx "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/geomx-ngs/current/). | +| [HiFi](https://www.researchgate.net/publication/370676672_HiFi-Slide_spatial_RNA-Sequencing_v2) [](HiFi "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/hifi-slide/current/). | +| [Histology](https://en.wikipedia.org/wiki/Histology) [](Histology "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/histology/current/). | +| iCLAP [](iCLAP "Attribute description") | 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. | +| [IMC](https://docs.hubmapconsortium.org/assays/imc) [](IMC "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/imc-2d/current/). | +| [LC-MS](https://docs.hubmapconsortium.org/assays/lcms) [](LC-MS "Attribute description")| Coupling of liquid chromatography (LC) to mass spectrometry (MS). Link to [LC-MS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/lcms/current/). | +| [Light Sheet](https://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy) [](LightSheet "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/lightsheet/current/). | +| [MALDI-IMS](https://docs.hubmapconsortium.org/assays/maldi-ims) [](MALDI "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/maldi/current/). | +| [MIBI](https://www.researchgate.net/figure/Multiplexed-ion-beam-imaging-workflow-for-high-resolution-spatial-proteomics-Here_fig1_349770840) [](MIBI "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/mibi/current/). | +| [MERFISH](https://pubmed.ncbi.nlm.nih.gov/27241748/) [](MERFISH "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/merfish/current/). | +| [MUSIC](https://www.nature.com/articles/s41586-024-07239-w) [](MUSIC "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/music/current/). | +| [MxIF](https://pmc.ncbi.nlm.nih.gov/articles/PMC9959383/#) [](ThickSectionMultiphotonMxIF "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/thick-section-multiphoton-mxif/current/).| +| Pixel-seqV2 [](Pixel-seqV2 "Attribute description") | 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](https://docs.hubmapconsortium.org/assays/rnaseq) [](RNAseq "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq/current/).| +| [RNAseq with Probes](https://pmc.ncbi.nlm.nih.gov/articles/PMC5717752/#) [](RNAseqWithProbes "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq-with-probes/current/).| +| Raman-Imaging [](Raman-Imaging "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/raman-imaging/current/). | +| [SHG](https://en.wikipedia.org/wiki/Second-harmonic_imaging_microscopy) [](SecondHarmonicGeneration "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/second-harmonic-generation/current/).| +| [SeqFISH](https://docs.hubmapconsortium.org/assays/seqfish) [](seqFISH "Attribute description") | SeqFISH technology allows in situ imaging of multiple mRNAs using barcoding and fluorophore-labelled barcode readout-probes. Link to [SeqFISH directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/seqfish/). _The consortium is no longer accepting data of this type_.| +| [SIMS](https://www.frontiersin.org/journals/chemistry/articles/10.3389/fchem.2023.1237408/full) [](SIMS "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/sims/current/ "directory schema").| +| [Slide-seq](https://www.nature.com/articles/s41587-020-0739-1) [](Slide-seq "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/slide-seq/current/).| +| [SnareSeq2](https://www.nature.com/articles/s41596-021-00507-3) [](SnareSeq2 "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/snareseq2/current/).| +| STARmap [](STARmap "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/starmap/current/). | +| [Visium No Probes](https://ostr.ccr.cancer.gov/emerging-technologies/spatial-biology/visium/) [](VisiumNoProbes "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/visium-no-probes/current/). | +| [Visium with Probes](https://ngisweden.scilifelab.se/methods/10x-genomics-visium-cytassist-for-ffpe-samples/) [](VisiumWithProbes "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/visium-with-probes/current/). | +| [WGS](https://en.wikipedia.org/wiki/Whole_genome_sequencing) [](WGS "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/wgs/). _The consortium is no longer accepting data of this type_. | + + diff --git a/docs/assays/metadata/new-metadata-test.md b/docs/assays/metadata/new-metadata-test.md deleted file mode 100644 index a194bf5..0000000 --- a/docs/assays/metadata/new-metadata-test.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -layout: page ---- -## HuBMAP Metadata by Dataset Type - -A list of available dataset types (data types from multiple supported assays), with a link [](EnhancedSRS "Attribute description") 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](https://hubmapconsortium.github.io/ingest-validation-tools/4i/current/) [](4i "Attribute description")| 4i, or Iterative Indirect Immunofluorescence Imaging, is a high-resolution technique for imaging proteins within cells and tissues. | -| [Autofluorescence (AF)](https://docs.hubmapconsortium.org/assays/af) [](AutoFluorescence "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/af/current/). | -| [ATACseq](https://docs.hubmapconsortium.org/assays/atacseq) [](ATACseq "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/atacseq/current/). | -| [CODEX](https://docs.hubmapconsortium.org/assays/codex) [](CODEX "Attribute description")| Co-detection by indexing (CODEX) is a strategy for generating highly multiplexed images of fluorescently-labeled antigens. Link to [CODEX directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/codex/current/). | -| COMET [](COMET "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/cosmx-proteomics/current/) [](CosMx Proteomics "Attribute description")| 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. | -| [DESI](https://pmc.ncbi.nlm.nih.gov/articles/PMC6053038/) [](DESI "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/desi/current/). | -| [Enhanced SRS](https://www.nature.com/articles/s41467-019-13230-1) [](EnhancedSRS "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/enhanced-srs/current/). | -| [GeoMx](https://nanostring.com/products/geomx-digital-spatial-profiler/spatial-multiomics-enabled-with-geomx-dsp/) [](GeoMx "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/geomx-ngs/current/). | -| [HiFi-Slide](https://www.researchgate.net/publication/370676672_HiFi-Slide_spatial_RNA-Sequencing_v2) [](HiFi "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/hifi-slide/current/). | -| [Histology](https://en.wikipedia.org/wiki/Histology) [](Histology "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/histology/current/). | -| iCLAP [](iCLAP "Attribute description") | 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. | -| [IMC](https://docs.hubmapconsortium.org/assays/imc) [](IMC "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/imc-2d/current/). | -| [LC-MS](https://docs.hubmapconsortium.org/assays/lcms) [](LC-MS "Attribute description")| Coupling of liquid chromatography (LC) to mass spectrometry (MS). Link to [LC-MS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/lcms/current/). | -| [Light Sheet](https://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy) [](LightSheet "Attribute description")| 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](https://hubmapconsortium.github.io/ingest-validation-tools/lightsheet/current/). | -| [MALDI-IMS](https://docs.hubmapconsortium.org/assays/maldi-ims) [](MALDI "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/maldi/current/). | -| Multiplex Ion Beam Imaging
[(MIBI)](https://www.researchgate.net/figure/Multiplexed-ion-beam-imaging-workflow-for-high-resolution-spatial-proteomics-Here_fig1_349770840) [](MIBI "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/mibi/current/). | -| Multiplexed Error-Robust Fluorescence In Situ Hybridization [(MERFISH)](https://pubmed.ncbi.nlm.nih.gov/27241748/) [](MERFISH "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/merfish/current/). | -| Multiplexed Universal Single-cell Chromatin and RNA interactions [(MUSIC)](https://www.nature.com/articles/s41586-024-07239-w) [](MUSIC "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/music/current/). | -| [RNAseq](https://docs.hubmapconsortium.org/assays/rnaseq) [](RNAseq "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq/current/).| -| [RNAseq with Probes](https://pmc.ncbi.nlm.nih.gov/articles/PMC5717752/#) [](RNAseqWithProbes "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq-with-probes/current/).| -| Raman-Imaging [](Raman-Imaging "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/raman-imaging/current/). | -| Second Harmonic Generation [(SHG)](https://en.wikipedia.org/wiki/Second-harmonic_imaging_microscopy) [](SecondHarmonicGeneration "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/second-harmonic-generation/current/).| -| Sequenced Fluorescence In Situ Hybridization [(SeqFISH)](https://docs.hubmapconsortium.org/assays/seqfish) [](seqFISH "Attribute description") | SeqFISH technology allows in situ imaging of multiple mRNAs using barcoding and fluorophore-labelled barcode readout-probes. Link to [SeqFISH directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/seqfish/). _The consortium is no longer accepting data of this type_.| -| [SIMS](https://www.frontiersin.org/journals/chemistry/articles/10.3389/fchem.2023.1237408/full) [](SIMS "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/sims/current/ "directory schema").| -| [Slide-seq](https://www.nature.com/articles/s41587-020-0739-1) [](Slide-seq "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/slide-seq/current/).| -| [SnareSeq2](https://www.nature.com/articles/s41596-021-00507-3) [](SnareSeq2 "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/snareseq2/current/).| -| STARmap [](STARmap "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/starmap/current/). | -| Thick Section Multiphoton
[(TSM) MxIF](https://pmc.ncbi.nlm.nih.gov/articles/PMC9959383/#) [](ThickSectionMultiphotonMxIF "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/thick-section-multiphoton-mxif/current/).| -| [Visium No Probes (NP)](https://ostr.ccr.cancer.gov/emerging-technologies/spatial-biology/visium/) [](VisiumNoProbes "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/visium-no-probes/current/). | -| [Visium with Probes](https://ngisweden.scilifelab.se/methods/10x-genomics-visium-cytassist-for-ffpe-samples/) [](VisiumWithProbes "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/visium-with-probes/current/). | -|Whole Genome Sequencing
[(WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) [](WGS "Attribute description") | 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](https://hubmapconsortium.github.io/ingest-validation-tools/wgs/). _The consortium is no longer accepting data of this type_. | - -#### Commentary: -Fellow **Documentation Team** members, this page is a "mock-up" of the _updated_ [HuBMAP Metadata by Dataset page](https://docs.hubmapconsortium.org/assays/metadata/)