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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
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Updated: Jul 10, 2025

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing
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Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing

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Single-Nucleus RNA-Sequencing in Brain Tissue.

Rebecca Waag1,2, Johannes Bohacek1,2

  • 1Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.

Current Protocols
|November 21, 2023
PubMed
Summary
This summary is machine-generated.

Single-nucleus RNA sequencing offers a robust alternative to single-cell methods for brain tissue analysis. This protocol details nuclei preparation for cell type-specific transcriptional profiling, overcoming cell-based limitations.

Keywords:
brainmousesequencingsingle-nucleustranscriptomics

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Area of Science:

  • Neuroscience
  • Genomics
  • Molecular Biology

Background:

  • Single-cell sequencing is vital for neuroscience, but cell preparation is challenging and can affect results.
  • Single-cell suspensions have limitations impacting transcriptional data accuracy.
  • Single-nucleus sequencing presents an alternative to address these preparation challenges.

Purpose of the Study:

  • To provide a detailed protocol for preparing single-nucleus suspensions.
  • To enable cell type-specific transcriptional profiling of brain tissue.
  • To optimize single-nucleus RNA sequencing using the 10x Genomics platform.

Main Methods:

  • Developed a protocol for single-nucleus suspension preparation from brain tissue.
  • Adapted the 10x Genomics single-cell gene expression assay for nuclei.
  • Included guidelines for experimental design and data analysis for single-nucleus RNA sequencing.

Main Results:

  • Successfully generated a protocol for single-nucleus suspension suitable for RNA sequencing.
  • Demonstrated the utility of single-nucleus RNA sequencing for transcriptional profiling.
  • Highlighted critical considerations for successful experimental design and data interpretation.

Conclusions:

  • Single-nucleus RNA sequencing is a viable and advantageous method for brain tissue analysis.
  • The provided protocol facilitates robust cell type-specific transcriptional profiling.
  • This approach overcomes limitations associated with traditional single-cell preparation methods.