assay

The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both ‘scRNASeq’ and ‘CITESeq’.

Valid value descriptions created by ChatGPT 4o

Valid Values	Description	Source
ASAPSeq	ATAC with Select Antigen Profiling by sequencing. A multimodal high-throughput single-cell method that simultaneously measures protein levels and chromatin accessibility.	General knowledge
CE-MS	Capillary Electrophoresis-Mass Spectrometry. An analytical technique combining capillary electrophoresis with mass spectrometry to separate and identify molecules, often used in proteomics and metabolomics.	General knowledge
CITESeq	Cellular Indexing of Transcriptomes and Epitopes by Sequencing. A method that enables simultaneous measurement of protein and RNA expression in single cells by using oligonucleotide-labeled antibodies.	Wikipedia
CosMX	A spatial molecular imaging platform that provides high-plex in situ analysis at cellular and subcellular resolution, enabling rapid quantification and visualization of RNA and protein analytes in tissue samples.	NanoString
CyTOF	Cytometry by Time-Of-Flight. A mass cytometry technique that uses metal-tagged antibodies to detect multiple parameters in single cells, allowing for high-dimensional analysis of cell populations.	Wikipedia
H&E	Hematoxylin and Eosin Staining. A widely used staining technique in histology to distinguish between different tissue structures by staining nuclei blue (hematoxylin) and cytoplasm and extracellular matrix pink (eosin).	General knowledge
LC-MS/MS	Liquid Chromatography-Tandem Mass Spectrometry. An analytical technique combining liquid chromatography with tandem mass spectrometry to separate and identify compounds in complex mixtures, commonly used in proteomics and metabolomics.	General knowledge
NULISA
Olink Explore HT
RNASeq	A next-generation sequencing technique used to analyze the quantity and sequences of RNA in a sample, providing insights into gene expression and transcriptome profiling.	General knowledge
SNP array
SomaScan	A proteomics platform that uses modified DNA aptamers to measure protein concentrations in biological samples, enabling large-scale protein biomarker discovery.	General knowledge
VDJSeq	A sequencing method focused on profiling the variable (V), diversity (D), and joining (J) gene segments of immune receptors, providing insights into immune diversity and clonality.	General knowledge
WES	Whole Exome Sequencing. A genomic technique for sequencing all the protein-coding regions (exons) of genes in a genome, used to identify genetic variants associated with diseases.	General knowledge
WGS	Whole Genome Sequencing. A comprehensive method for sequencing the entire DNA content of an organism's genome, providing detailed information on genetic variations.	General knowledge
Xenium	A spatial transcriptomics platform that enables high-resolution mapping of gene expression within tissue sections, providing insights into spatial gene activity.	General knowledge
feature barcode sequencing	A method that allows for the simultaneous measurement of multiple modalities, such as gene expression and protein levels, in single cells by using barcoded antibodies or other markers.	General knowledge
flow cytometry	A technology used to analyze the physical and chemical characteristics of cells or particles as they flow in a fluid stream through a beam of light, enabling multiparametric analysis of cell populations.	General knowledge
imaging mass cytometry	A technique that combines mass spectrometry with imaging to analyze multiple protein expressions in tissue sections at subcellular resolution, providing spatial and quantitative data.	Springer
imaging mass spectrometry	An analytical technique that combines imaging and mass spectrometry to visualize the spatial distribution of molecules, such as metabolites and proteins, within biological samples.	General knowledge
multiplexed ELISA	Multiplexed Enzyme-Linked Immunosorbent Assay. An assay technique that allows for the simultaneous detection and quantification of multiple analytes (e.g., proteins, antibodies) in a single sample, increasing throughput and efficiency.	General knowledge
scRNASeq	Single-cell RNA-sequencing. A technique that profiles gene expression at the single-cell level, providing insights into cellular heterogeneity and function within complex tissues.	General knowledge
scVDJSeq	A method that sequences the variable regions of immune receptor genes in single cells, enabling analysis of immune repertoire diversity and clonality.	General knowledge
serial IHC
snATACSeq	Single-nucleus Assay for Transposase-Accessible Chromatin using Sequencing. A method that profiles chromatin accessibility in isolated nuclei, providing insights into gene regulatory elements and epigenetic landscapes at single-cell resolution.	General knowledge
snRNASeq	Single-nucleus RNA Sequencing. A technique that profiles gene expression in isolated nuclei from tissues, useful for studying cells that are difficult to dissociate or in preserved samples.	General knowledge