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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...

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Related Experiment Video

Updated: Jun 14, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

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CellSP: Module discovery and visualization for subcellular spatial transcriptomics data.

Bhavay Aggarwal1, Saurabh Sinha1,2

  • 1The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

Biorxiv : the Preprint Server for Biology
|January 27, 2025
PubMed
Summary
This summary is machine-generated.

We developed CellSP, a computational tool to identify and interpret spatial patterns of messenger RNA (mRNA) within cells. This framework reveals gene-cell modules linked to biological functions across various tissues and diseases.

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Area of Science:

  • Molecular Biology
  • Computational Biology
  • Genomics

Background:

  • Spatial transcriptomics allows studying mRNA distribution within cells, crucial for cellular function.
  • Existing tools lack the capability to identify and interpret functionally relevant spatial patterns of subcellular transcript distribution.

Purpose of the Study:

  • To present CellSP, a computational framework for identifying, visualizing, and characterizing consistent subcellular spatial patterns of mRNA.
  • To introduce the concept of "gene-cell modules" with coordinated subcellular transcript distributions.

Main Methods:

  • Development of the CellSP computational framework.
  • Utilizing gene-cell modules to represent coordinated transcript distributions.
  • Visualization and functional interpretation of spatial patterns.

Main Results:

  • CellSP reliably identifies functionally significant modules across diverse tissues and technologies.
  • Discovery of subcellular spatial phenomena related to myelination, axonogenesis, and synapse formation in the mouse brain.
  • Identification of immune response modules in kidney cancer and myelination modules in Alzheimer's disease models.

Conclusions:

  • CellSP provides a robust method for analyzing subcellular transcript spatial patterns.
  • The framework offers functional insights into gene-cell modules.
  • CellSP facilitates discoveries in neuroscience and disease research.