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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: May 7, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
09:58

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SpaceBar enables clone tracing in spatial transcriptomic data.

Grant Kinsler1, Caitlin Fagan1, Haiyin Li2

  • 1Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.

Biorxiv : the Preprint Server for Biology
|February 24, 2025
PubMed
Summary
This summary is machine-generated.

SpaceBar enables simultaneous clone tracing and spatial transcriptomics profiling using synthetic barcodes. This method distinguishes clonal dynamics from environmental signals in complex tissues.

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Area of Science:

  • Cellular and Molecular Biology
  • Genomics and Bioinformatics
  • Cancer Research

Background:

  • Understanding cellular heterogeneity and spatial organization is crucial in complex tissues.
  • Simultaneous tracing of cell clones and their spatial gene expression remains a challenge.
  • Existing methods lack the ability to differentiate intrinsic clonal behavior from extrinsic environmental influences.

Purpose of the Study:

  • To introduce SpaceBar, a novel cellular barcoding strategy for simultaneous clone tracing and spatial transcriptomics.
  • To develop a framework for dissecting clonal dynamics and environmentally-driven transcriptional regulation.
  • To quantify the drivers of gene expression in complex tissue microenvironments.

Main Methods:

  • Development of a 96-synthetic barcode library for cellular labeling.
  • Integration of SpaceBar with imaging-based spatial transcriptomics (seqFISH).
  • Application in a melanoma tumor xenograft model to profile clone identity and spatial gene expression.
  • Creation of a gene scoring metric to assess intrinsic vs. extrinsic regulation of gene expression.

Main Results:

  • Successful simultaneous labeling of melanoma cells with combined barcodes.
  • In situ profiling of clone identity and spatial gene expression within the tumor xenograft.
  • Quantification of gene expression drivers, distinguishing cellular cues from environmental signals.
  • Demonstration of the framework's ability to separate clonal dynamics from environmental transcriptional regulation.

Conclusions:

  • SpaceBar provides a powerful tool for high-resolution analysis of clonal evolution and spatial gene expression.
  • The developed gene scoring metric effectively differentiates intrinsic and extrinsic factors influencing cellular phenotypes.
  • This approach offers new insights into complex tissue contexts and cellular behavior in disease models.