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http://purl.obolibrary.org/obo/IAO_0000123

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.

https://doi.org/10.1016/j.cell.2015.05.002

sequencing assay

http://purl.obolibrary.org/obo/IAO_0000123

A sequencing assay that uses fluorescent probes that bind to parts of a nucleic acid sequence that have a high degree of sequence complementarity. Fluorescence microscopy can be used to find out where the fluorescent probes is bound on the chromosomes.

http://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization

sequencing assay

http://purl.obolibrary.org/obo/IAO_0000123

An imaging assay that uses micro-optical sectioning tomography technology combined with fluorescence molecular labeling of neuronal projections.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701528/

fluorescence microscopy

http://purl.obolibrary.org/obo/IAO_0000123

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

http://purl.obolibrary.org/obo/IAO_0000123

MORF genetic sparse labeling

A neuron morphology assay where sparse and stochastic that involves the labeling of genetically-defined neurons.

http://doi.org/10.1038/nprot.2014.114

neuron morphology assay

serial two-photon tomography

http://purl.obolibrary.org/obo/IAO_0000123

An imaging assay 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.

http://doi.org/10.1038/nmeth.1854

http://purl.obolibrary.org/obo/IAO_0000123

A serial two photon tomography assay that produces images of mouse brains with sufficient detail to represent axons of individual neurons.

http://www.janelia.org/project-team/mouselight/research

serial two-photon tomography assay

multi-electrode extracellular electrophysiology

http://purl.obolibrary.org/obo/IAO_0000123

An electrophysiological assay that employs many electrodes to record extracellular field potentials.

http://en.wikipedia.org/wiki/Microelectrode_array

electrophysiological assay

http://purl.obolibrary.org/obo/IAO_0000123

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

3D structure determination assay

http://purl.obolibrary.org/obo/IAO_0000123

A sequencing assay wherein a patch clamp recording is taken from a neuron and then scRNA sequencing is performed on the cell soma.

http://doi.org/10.1038/nprot.2017.120

sequencing assay

retrograde tracing

http://purl.obolibrary.org/obo/IAO_0000123

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.

PERSON: Patrick Ray

retrograde transsynaptic tracing

http://purl.obolibrary.org/obo/IAO_0000123

An assay that traces the neural connections from a synapse to a soma allowing th mapping of connections between neurons in a structure and a target in the brain.

http://en.wikipedia.org/wiki/Retrograde_tracing

retrograde tracing assay

sequential fluorescence in situ hybridization

http://purl.obolibrary.org/obo/IAO_0000123

An assay where transcripts are labeled with fluorescent probes in sequential rounds of hybridization to read out the temporal barcode for each transcript. The temporal barcodes can then be decoded to uniquely identify the RNA transcripts present in the sample. RNA can be identified directly in a variety of samples from extracted RNA to tissues.

http://www.seqfish.com/technology

Definition needs curation

switching mechanism at the 5' end of RNA template

http://purl.obolibrary.org/obo/IAO_0000123

A single cell sequencing assay wherein the target cells are lysed, and the RNA is hybridized to an oligo(dT)-containing primer. The first strand of the cDNA is synthesized with the addition of a few untemplated C nucleotides. This poly(C) overhang is added exclusively to full-length transcripts. An oligonucleotide primer is hybridized to the poly(C) overhang and used to synthesize the second strand. Full-length cDNAs are PCR-amplified to obtain nanogram amounts of DNA. The PCR products are purified for sequencing.

http://www.enseqlopedia.com/wiki-entry/rna-sequencing-methods/low-level-rna-detection/smart-seq/

Definition needs curation

sequencing assay

switching mechanism at the 5' end of RNA template v4

http://purl.obolibrary.org/obo/IAO_0000123

A switching mechanism at the 5' end of RNA template sequencing assay that is the fourth version of such an assay.

PERSON: Patrick Ray

switching mecahnism at the 5' end of RNA template assay

tracing the relationship between input and output

http://purl.obolibrary.org/obo/IAO_0000123

An experimental protocol where complementary viruses are injected into brain regions to monosynaptically label inputs to a specific projection neuron population.

http://cic.ini.usc.edu/protocols/trio-tracing

experimental protocol

http://purl.obolibrary.org/obo/IAO_0000123

light sheet microscopy

An assay that uses a laser light-sheet to illuminate a region of a sample that has been treated to excite fluorescently.

http://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy

fluorescence microscopy

cre-dependent anterograde tracing

http://purl.obolibrary.org/obo/IAO_0000123

An anterograde tracing assay that uses a Cre recombinase-dependent as a tracer.

http://doi.org/10.1016/j.neuron.2011.12.002

anterograde tracing assay

anterograde tracing

http://purl.obolibrary.org/obo/IAO_0000123

A tract tracing method that labels axons and their terminations either by anterograde axonal transport or degeneration.

PERSON: mihailbota

Definition needs curation

*should be tract tracing assay*

optical coherence tomography

http://purl.obolibrary.org/obo/IAO_0000123

An imaging assay that has as an output label-free, cross-sectional imaging of biological tissue microstructure using tissue backscattering properties.

PMID: 29214158|doi: 10.1155/2017/3409327

volumetric imaging with synchronized on-the-fly oblique-scan and readout assay

http://purl.obolibrary.org/obo/IAO_0000123

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

light sheet microscopy assay

single-nucleus chromatin accessibility and mRNA expression sequencing assay

http://purl.obolibrary.org/obo/IAO_0000123

SNARE-seq2|SNARE-seq2 assay

A sequencing assay that involves the isolation of single nuclei and open chromatin tagmentation in the isolated nuclei using a transposase. The tagmented nuclei are then encapsulated in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which links the tagmented gDNA fragments to the bead, enabling the bead to capture both mRNAs and open chromatin fragments. After mRNAs and gDNA fragments are released from the bead by heating, RT and PCR amplification are performed to generate a library of cDNA and open chromatin gDNA fragments.

https://doi.org/10.1038/s12276-020-0420-2

Definition needs curation

sequencing assay

composite in situ imaging

http://purl.obolibrary.org/obo/IAO_0000123

An imaging 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

switching mechanism at the 5' end of RNA template sequencing assay 2

http://purl.obolibrary.org/obo/IAO_0000123

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.

https://doi.org/10.1038/nprot.2014.006

switching mechanism at the 5' end of RNA template sequencing assay