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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: May 14, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
10:45

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Protein-guided RNA barcoding links transcriptomes to synaptic architecture.

Amanda Urke, Michael-John Dolan, Jonah Silverman

    Biorxiv : the Preprint Server for Biology
    |May 13, 2026
    PubMed
    Summary
    This summary is machine-generated.

    Synapse-seq is a new in vivo genomics method that links neuron transcriptomes to their synaptic connections. This approach maps brain circuits and reveals cell-type specific wiring patterns.

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    Last Updated: May 14, 2026

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    Area of Science:

    • Neuroscience
    • Genomics
    • Molecular Biology

    Background:

    • Mammalian brain function depends on intricate synaptic connections between diverse cell types.
    • Existing methods struggle to link neuronal transcriptomic data with precise neuroanatomical information.
    • Scalable techniques are needed to map neuronal connectivity and molecular identity simultaneously.

    Purpose of the Study:

    • To develop and validate Synapse-seq, a novel in vivo strategy for linking transcriptomic profiles with synaptic organization.
    • To investigate the neuroanatomical organization of specific brain circuits in the mouse.
    • To explore cell type-specific variations in dendritic architecture.

    Main Methods:

    • Synapse-seq utilizes adeno-associated virus (AAV) delivery to route cell-identifying barcoded messenger RNAs (mRNAs) to subcellular compartments.
    • Barcodes are targeted to presynaptic terminals using synaptophysin or to postsynaptic sites via nanobodies targeting PSD95.
    • Single-cell and spatial genomics techniques are employed for barcode detection and analysis.

    Main Results:

    • Presynaptic Synapse-seq in the visual cortex identified known projections and novel cortical layer subtypes with specific thalamic innervation.
    • Analysis of corticostriatal innervation revealed topographic rules for intratelencephalic and extratelencephalic neurons.
    • Postsynaptic barcoding in the hippocampus demonstrated cell type-specific dendritic architecture variations.

    Conclusions:

    • Synapse-seq provides a versatile, genomics-based platform for integrated analysis of molecular identity and synaptic organization.
    • The method enables high-resolution mapping of neuronal connectivity and circuit architecture.
    • This approach advances our understanding of mammalian brain organization at the molecular and anatomical levels.