| ID |
A rdfs:label |
A alternative term SPLIT=| |
A definition SPLIT=| |
A definition source SPLIT=| |
| OBI:0003376 |
droplet-based single-cell RNA sequencing assay |
Dropseq |
A sequencing assay that analyzes mRNA transcripts from droplets of individual cells. The droplets are compartmentalized via a microfluidic device. After the cells are compartmentalized, cells in droplets are lysed and the released mRNA hybridizes to the oligo(dT) tract of the primer beads. Then the droplets are pooled and broken to release the beads which are then isolated and reverse-transcribed with template switching. The resulting cDNA strands are PCR-amplified and the sequencing adapters are added. The barcoded mRNA samples are then sequenced. |
url:https://doi.org/10.1016/j.cell.2015.05.002 |
| OBI:0003094 |
fluorescence in-situ hybridization assay |
FISH |
An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. |
url:https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization |
| BITO:0000001 |
fluorescence micro-optical sectioning tomography assay |
fMOST |
An imaging assay that uses micro-optical sectioning tomography technology combined with fluorescence molecular labeling of neuronal projections. |
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701528/ |
| BITO:0000002 |
multiplexed error-robust fluorescence in situ hybridization assay |
MERFISH |
An imaging assay that measures the copy number and spatial distribution of hundreds to thousands of RNA species in single cells. |
DOI: 10.1126/science.aaa6090 |
| OBI:0003124 |
neuron morphology assay |
|
A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. |
Patrick Ray |
| OBI:0003125 |
mosaicism with repeat frameshift genetic sparse labeling |
MORF genetic sparse labeling |
A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. |
https://doi.org/10.1016/j.neuron.2020.07.019|https://biccn.org/teams/u01-yang |
| BITO:0000003 |
serial two-photon tomography assay |
STPT |
A fluorescence microscopy that generates high-throughput flourescence imaging of mouse brains by integrating two-photon microscopy and tissue sectioning. Serial two-photon tomography generates high-resolution datasets. |
url:http://doi.org/10.1038/nmeth.1854 |
| BITO:0000004 |
mouselight assay |
|
A serial two photon tomography assay that produces images of mouse brains with sufficient detail to represent axons of individual neurons. |
url:http://www.janelia.org/project-team/mouselight/research |
| BITO:0000005 |
multi-electrode extracellular electrophysiology assay |
|
An electrophysiology assay that employs many electrodes to record extracellular field potentials. |
url:http://en.wikipedia.org/wiki/Microelectrode_array |
| OBI:0003126 |
neuron morphology reconstruction assay |
|
A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). |
http://doi.org/10.1101/675280 |
| OBI:0003375 |
patch clamp single-cell RNA sequencing assay |
patch-seq|patch clamp sequencing assay |
A single-cell RNA sequencing assay wherein a patch clamp recording is taken from a neuron and then scRNA sequencing is performed on the cell soma. |
url:http://doi.org/10.1038/nprot.2017.120 |
| OBI:0003104 |
single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing |
sciATACseq |
An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. |
url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300/ |
| OBI:0003105 |
single-cell combinatorial indexing RNA sequencing assay |
sciRNAseq |
A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. |
url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894354/ |
| OBI:0003106 |
sequential fluorescence in-situ hybridization assay |
seqFISH |
A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. |
url:https://spatial.caltech.edu/seqfish/ |
| OBI:0003107 |
slide-seq assay |
|
An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. |
url:https://science.sciencemag.org/content/363/6434/1463 |
| OBI:0003108 |
single-nucleus chromatin accessibility and mRNA expression sequencing assay |
SNAREseq|SNARE-seq |
A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. |
url:https://www.nature.com/articles/s41587-019-0290-0 |
| OBI:0003109 |
single-nucleus RNA sequencing assay |
single nuclei RNA sequencing|sNuc-seq|snRNA-seq |
A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. |
EFO:0009809|url:https://www.biocompare.com/Editorial-Articles/557506-Advantages-of-Single-Nucleus-RNA-Sequencing/ |
| OBI:0003095 |
decoding amplified targeted transcripts with fluorescence in situ hybridization assay |
DARTFISH |
A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. |
url:https://escholarship.org/uc/item/5bq3128f|url:http://genome-tech.ucsd.edu/ZhangLab/index.php/data/tech-dev/|url:http://www.weizmann.ac.il/conferences/SCG2015/sites/conferences.SCG2015/files/scg_2015_abstractbook_online_version.pdf |
| OBI:0003089 |
bulk assay for transposase-accessible chromatin using sequencing |
bulk ATAC-seq |
An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. |
PMID:24097267 |
| OBI:0002764 |
single-cell ATAC-seq |
scATAC-seq |
An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. |
http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html |
| OBI:0002762 |
single-nucleus ATAC-seq |
snATAC-seq |
An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. |
http://www.biorxiv.org/content/early/2017/07/06/159137 |
| OBI:0002631 |
single-cell RNA sequencing assay |
scRNA-seq |
An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. |
Anna Maria Masci |
| BITO:0000006 |
retrograde tracing assay |
retrograde tracing|retrograde labeling |
An assay wherein a substance is taken up by an axon terminal and transported toward the soma to mark (or trace) some part of a cell. |
Patrick Ray |
| BITO:0000007 |
retrograde transsynaptic tracing assay |
|
A retrograde tracing assay that traces the neural connections from a synapse to a soma allowing the mapping of connections between neurons in a structure and a target in the brain. |
url:http://en.wikipedia.org/wiki/Retrograde_tracing |
| OBI:0003378 |
switching mechanism at the 5' end of RNA template sequencing assay |
SMARTseq|SMART seq |
A single cell sequencing assay wherein cells are lysed and their recovered RNA is hybridized to an oligo(dT) that primes a reverse transcription reaction, the outcome of which are cDNA’s that have PCR handles on both ends. The cDNA's are then amplified using PCR, and the products are sequenced. |
url:http://www.enseqlopedia.com/wiki-entry/rna-sequencing-methods/low-level-rna-detection/smart-seq/< |
| OBI:0003379 |
switching mechanism at the 5' end of RNA template sequencing 2 assay |
SMARTseq2 |
A switching mechanism at the 5' end of RNA template sequencing assay that allows the generation of full-length cDNA and sequencing libraries by using standard reagents. |
|
| OBI:0003377 |
single-nucleus chromatin accessibility and mRNA expression sequencing 2 assay |
SNARE-seq2|SNARE-seq2 assay |
A sequencing assay that genrates a library of cDNA and open chromatin gDNA fragments by tagmenting a single nuclei and open chromatin, and encapsulating those in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which links the tagmented gDNA fragments to the bead which capture both mRNAs and open chromatin fragments. |
|
| BITO:0000008 |
switching mechanism at the 5' end of RNA template sequencing assay v4 |
SMARTseq v4 |
A switching mechanism at the 5' end of RNA template sequencing assay that is the fourth version of such an assay. |
|
| BITO:0000009 |
tracing the relationship between input and output study design |
TRIO tracing |
A study design in which complementary viruses are to be injected into brain regions to monosynaptically label inputs to a specific projection neuron population. |
url:http://cic.ini.usc.edu/protocols/trio-tracing |
| OBI:0003098 |
lightsheet fluorescence microscopy assay |
|
A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. |
url:https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/light-sheet-fluorescence-microscopy |
| BITO:0000010 |
cre-dependent anterograde tracing assay |
|
An anterograde tracing assay that uses a Cre recombinase-dependent as a tracer. |
url:http://doi.org/10.1016/j.neuron.2011.12.002 |
| BITO:0000011 |
anterograde tracing assay |
|
An assay wherein axon projections are traced from their source (cell body or soma) to their point of termination (synapse). |
url:https://en.wikipedia.org/wiki/Anterograde_tracing |
| BITO:0000012 |
optical coherence tomography assay |
OCT |
An imaging assay that has as an output label-free, cross-sectional imaging of biological tissue microstructure using tissue backscattering properties. |
doi: 10.1155/2017/3409327 |
| BITO:0000013 |
volumetric imaging with synchronized on-the-fly oblique-scan and readout assay |
VISoR|VISoR assay |
A light sheet microscopy assay that combines synchronized scanning illumination and oblique imaging over cleared, thick tissue sections in smooth motion that produces a 3D image of a brain. |
doi: 10.1093/nsr/nwz053 |
| BITO:0000014 |
composite in situ imaging |
CISI |
A fluorescence microscopy assay wherein fluorescence in situ hybridization is leveraged with multiplexed analysis that uses each channel to measure the composite (sum) abundances of multiple genes in each channel and decompresses and determines individual gene level. |
DOI: 10.1101/743039 |
| BITO:0000015 |
3-level single-cell combinatorial indexing RNA sequencing assay |
sci-RNA-seq3|3-level sci-RNA-seq |
A RNA sequencing assay that involves three levels of indexing. |
https://www.protocols.io/view/sci-rna-seq3-9yih7ue |
| BITO:0000016 |
3-level single-cell combinatorial indexing ATAC sequencing assay |
sci-ATAC-seq3|3-level sci-ATAC-seq |
An ATAC-seq assay that involves single-cell combinatorial indexing at three levels. |
https://www.protocols.io/view/sci-atac-seq3-be8mjhu6 |
| BITO:0000017 |
10X chromium ATAC-seq assay |
10X chromium ATAC-seq|10X chromium ATAC sequencing assay |
An ATAC-seq assay that involves use of the 10x sequencing technology assay for transposase-accessible chromatin using sequencing (ATAC-seq). |
|
| BITO:0000018 |
SHARE-seq assay |
SHARE-seq |
A RNA-seq assay that uses high-throughput ATAC and RNA expression with sequencing to measure chromatin accessibility and gene expression in the same single cell. |
https://doi.org/10.1016/j.cell.2020.09.056 |
| BITO:0000019 |
single cell multiome ATAC + gene expression assay |
single cell multiome ATAC + gene expression |
An ATAC-seq assay that provides information about both transcriptome and epigenome from a single cell. |
https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression |
| BITO:0000020 |
double in vitro transcription with absoluted counts sequencing assay |
DIVA-seq |
A single-cell RNA sequencing assay wherein sparse fluorescently labeled single neurons are collected manually from freshly dissociated mouse brain tissue. Then single-labeled neurons with high purity are integrated with an in vitro transcription-based amplification protocol that preserves endogenous transcript ratios. Subsequently a double linear amplification method that uses unique molecule identifiers (UMIs) is used to generate individual mRNA counts. Two rounds of amplification follow. |
http://doi.org/10.3791/58690 |
| BITO:0000021 |
oblique light sheet tomography assay |
OLST |
A light sheet tomography assay wherein the sample is imaged from the top using oblique light sheet fluorescence microscopy illumination and detection strategy and the imaged top portion of the tissue is removed by vibratome sectioning. |
http://doi.org/10.17504/protocols.io.smwec7e |
| BITO:0000022 |
cyclic single-molecule fluorescence in situ hybridization assay |
osmFISH |
A cyclic single molecule fluorescent in situ hybridization assay used to quantify the expression level of specific transcripts in tissue sections by direct labeling of individual RNA molecules. |
http://doi.org/10.17504/protocols.io.psednbe |
| BITO:0000023 |
SNARE-seq2 (ATAC-seq) |
|
A SNARE-seq v2 assay that utilizes ATAC-seq as a part. |
|
| BITO:0000024 |
SNARE-seq2 (RNA-seq) |
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A SNARE-seq v2 assay that utilizes RNA-seq as a part. |
|
| BITO:0000025 |
nanopore DNA sequencing assay |
|
A DNA sequencing assay that provides direct, real-time analysis of long DNA or RNA fragments by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence. |
https://nanoporetech.com/applications/dna-nanopore-sequencing |
| BITO:0000026 |
single cell isoform RNA sequencing assay |
ScISOr-seq |
An isoform sequencing assay that begins with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting. |
https://doi.org/10.1038/nbt.4259 |
| BITO:0000027 |
single nucleus methyl-3C sequencing assay |
sn-m3c-seq |
A single-cell RNA sequencing assay that jointly profiles chromatin conformation and DNA methylation information from the same cell. |
https://doi.org/10.1038/s41592-019-0547-z |
| BITO:0000028 |
single nucleus methyl-C sequencing assay version 2 |
snmC-seq2 |
A library preparation method for single-nucleus methylome library preparation that provides significant improvements in read mapping, amount of artifactual reads, throughput, library complexity, and coverage uniformity over snmC-seq. |
|
| BITO:0000029 |
mC-seq3 |
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| BITO:0000030 |
single-cell combinatorial indexing with WGBS methylation analysis version 2 |
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The second version of the single-cell combinatorial indexing with WGBS methylation analysis. |
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| BITO:0000031 |
multiplex immunoassay |
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An immunoassay that uses magnetic beads to measure multiple analytes in a single assay. |
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| BITO:0000032 |
immunoassay |
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An assay that enables the presence or the concentration of a substance in a material to be measured by exploiting the specific binding between an analyte and the corresponding detection antibody. |
|
| BITO:0000033 |
calcium imaging assay |
Ca2+ imaging|Ca imaging |
An imaging assay that is designed to show the calcium (Ca2+) levels of a tissue or medium. |
http://en.wikipedia.org/wiki/Calcium_imaging|ERO:0000634 |
| BITO:0000034 |
cellular assay |
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An assay that generates data about the presence, quantity, structure, function, behavior, or activity of cells, or a process that occurs at a cellular level of anatomical granularity (includes subcellular structures and organelles). |
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| BITO:0000035 |
human brain optimized light sheet microscopy assay |
HOLiS |
A light sheet fluorescence microscopy assay that employs high-speed scanning single-objective light sheet imaging with spectral multiplexing and cell-type encoding. Human brain samples are processed using a clearing and immunostaining approach called HuB.Clear which can generate optically clear, 5 mm thick, whole-mount brain slabs. High-field magnetic resonance imaging (MRI) data acquired on the intact, fixed brain prior to sectioning will provide a vital cross-reference for comparison while also facilitating registration of data to a common coordinate frameworks. HOLiS data will be analyzed to extract cell locations and cell type identities, generating databases that can be compared to standard neuroanatomical atlases, while also permitting careful examination of brain-wide patterns and inter-subject differences. |
https://www.humanbrainmapping.org/files/2022/Annual%20Meeting%20Symposia/1511_Imaging_and_analysis_of_3D%5B1%5D.pdf |
| BITO:0000036 |
temp-O sequencing assay |
temp-O seq |
A RNA sequencing assay based on BioSpyder Technologies Templated Oligo Detection Assay that targets RNAs with detector olives and removes excess probes and enzymatic inhibitors before the first enzymatic step. Correctly hybridized detector olives are ligated, then amplified through primer landing sites that are share among all probes. |
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| BITO:0000037 |
x-ray holographic nano-tomography assay |
XHN |
A 3D structure determination assay that employs X-ray holographic nano-tomography to determine the three-dimensional structure of an entity. |
https://doi.org/10.1038/s41593-020-0704-9 |
| BITO:0000038 |
Pacific Bioscience long-read sequencing assay |
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A DNA sequencing assay wherein a single DNA polymerase enzyme is affixed at the bottom of a zero-mode waveguide (ZMW) with a single molecule of DNA as a template. The Pacific Biotechnologies version is a single-molecule real-time (SMRT) sequencing assay. The ZMW is a structure that creates an illuminated observation volume that is small enough to observe only a single nucleotide of DNA being incorporated by DNA polymerase. Each of the four DNA bases is attached to one of four different fluorescent dyes. When a nucleotide is incorporated by the DNA polymerase, the fluorescent tag is cleaved off and diffuses out of the observation area of the ZMW where its fluorescence is no longer observable. A detector detects the fluorescent signal of the nucleotide incorporation, and the base call is made according to the corresponding fluorescence of the dye. |
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| BITO:0000039 |
enhancer virus labelling assay |
enhancer virus labeling |
An imaging assay wherein chromatin accessibility data is collected from cells and enhancers specific to cell types are identified, cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, which drive trans gene expression in specific cell types. Then, an image of the marked cell class is generated through fluorescence microscopy. |
https://doi.org/10.1016/j.neuron.2021.03.011 |
| BITO:0000040 |
paired-tag assay |
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An ultra-high-throughput histone modification and transcriptome profiling assay that produces cell-type-resolved maps of chromatin state and transcriptome in complex tissues. |
https://doi.org/10.1038/s41592-021-01060-3 |
| OBI:0002117 |
whole genome sequencing assay |
WGS |
A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. |
PMID:25827230|PMID:23095910 |
| OBI:0002985 |
magnetic resonance imaging assay |
MRI |
An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. |
url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging |
| OBI:0000626 |
DNA sequencing assay |
nucleotide sequencing |
A sequencing assay which determines information on the sequence of a DNA molecule. |
url:https://en.wikipedia.org/wiki/DNA_sequencing |
| BITO:0000041 |
DBiT-seq |
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url:https://pubmed.ncbi.nlm.nih.gov/33188776/ |
| BITO:0000042 |
Perturb-seq |
CRISP-seq|CROP-seq |
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url:https://en.wikipedia.org/wiki/Perturb-seq |
| BITO:0000043 |
SMARTSeqSC |
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| BITO:0000044 |
SmartSeq3 |
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| BITO:0000045 |
10xV3.1 |
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| BITO:0000046 |
10xV3.1_HT |
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| BITO:0000047 |
10xMultiome;GEX |
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| BITO:0000048 |
10xMultiome;ATAC |
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| BITO:0000049 |
10xATAC_V2.0 |
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| BITO:0000050 |
10XMultiome-CellHashing;GEX |
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| BITO:0000051 |
10XMultiome-CellHashing;ATAC |
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| BITO:0000052 |
10XMultiome-Cell Hashing;Barcode |
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| BITO:0000053 |
10xV3.1_CellPlex;GEX |
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| BITO:0000054 |
10xV3.1_CellPlex;Barcode |
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| BITO:0000055 |
10xV3.1_HT_CellPlex;GEX |
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| BITO:0000056 |
10xV3.1_HT_CellPlex;Barcode |
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| BITO:0000057 |
MethylC-Seq |
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| BITO:0000058 |
snmCT-seq |
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| BITO:0000059 |
scATAC-seq |
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| BITO:0000060 |
Slide-seq MERFISH |
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| BITO:0000061 |
whole brain MERFISH |
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| BITO:0000062 |
DBiT RNA-seq |
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| BITO:0000063 |
DBiT ATAC-seq |
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| BITO:0000064 |
Slide-tag - spatial |
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| BITO:0000065 |
Slide-tag - GEX |
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| BITO:0000066 |
10X 5P V2 - GEX |
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| BITO:0000067 |
PIPseq T2 - 3P GEX |
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| BITO:0000068 |
PIPseq T20 - 3P GEX |
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| BITO:0000069 |
Slide-seq standard puck with 10X 5P v2 - GEX and spatial |
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