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Related Concept Videos

Eukaryotic Compartmentalizations01:46

Eukaryotic Compartmentalizations

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
For example, lysosomes in the animal cells...
Eukaryotic Compartmentalization01:46

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
For example, lysosomes in the animal cells...
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...
Eukaryotic Compartmentalization01:37

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
For example, lysosomes in the animal cells...
Entropy within the Cell01:22

Entropy within the Cell

A living cell's primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. None of the energy transfers in the universe are completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is...
Overview Of Cell Separation And Isolation01:20

Overview Of Cell Separation And Isolation

Cell separation was first achieved in 1964 by S. H. Seal, who separated large tumor cells from the smaller blood cells using filtration. Two years later, Pohl and Hawk performed experiments on how cells respond differently to a nonuniform electric field based on the cell type. Such observations were the inception of cell separation methods, which allow isolating a single cell type from a heterogeneous sample.

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Related Experiment Video

Updated: May 11, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.

Kimberle Shen1, Wan Yi Seow1, Choong Tat Keng1

  • 1Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, Republic of Singapore.

Nature Communications
|February 21, 2026
PubMed
Summary
This summary is machine-generated.

Spatial Perturb-Seq enables in vivo CRISPR screening of multiple genes in intact tissues. This method reveals cell-specific and microenvironmental impacts of gene knockouts, aiding neurodegenerative disease research.

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Last Updated: May 11, 2026

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Area of Science:

  • Genomics
  • Neuroscience
  • Molecular Biology

Background:

  • Understanding gene function in complex tissues is crucial for disease research.
  • Existing methods often struggle to maintain spatial context and cell representation during analysis.
  • Neurodegenerative diseases involve complex genetic and environmental interactions within the brain.

Purpose of the Study:

  • To develop a novel in vivo CRISPR technology for high-throughput functional genetic screening in intact tissues.
  • To investigate the cell-autonomous and cell-cell microenvironmental effects of gene knockouts relevant to neurodegenerative diseases.
  • To identify candidate genes involved in neuronal intercellular communication.

Main Methods:

  • Spatial Perturb-Seq: an in vivo CRISPR technology for interrogating multiple genes within single cells in intact tissues.
  • Compatibility with both sequencing-based and probe-based spatial technologies.
  • Application to knockout risk genes for neurodegenerative diseases in the mouse brain.

Main Results:

  • Successfully applied Spatial Perturb-Seq to functionally screen multiple genes in situ and in vivo.
  • Bypassed cell processing steps that can skew cell type representation, preserving tissue architecture.
  • Identified both intracellular and intercellular effects of gene knockouts.
  • Uncovered cell autonomous and cell-cell microenvironmental effects within the spatially intact mouse brain.
  • Identified candidate genes underlying dysregulated neuronal intercellular communication pathways.

Conclusions:

  • Spatial Perturb-Seq is a powerful tool for in vivo functional genomics in intact tissues.
  • The technology elucidates complex gene interactions and microenvironmental influences in neurodegenerative disease models.
  • This approach advances the study of neuronal communication and identifies potential therapeutic targets.