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Related Concept Videos

RNA-seq03:21

RNA-seq

9.9K
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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Ribosome Profiling02:24

Ribosome Profiling

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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...
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Related Experiment Video

Updated: Jun 25, 2025

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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A practical guide to spatial transcriptomics.

Lukas Valihrach1, Daniel Zucha2, Pavel Abaffy3

  • 1Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic; Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.

Molecular Aspects of Medicine
|May 22, 2024
PubMed
Summary
This summary is machine-generated.

Spatial transcriptomics enables detailed gene expression analysis in tissues. This review focuses on accessible commercial technologies, guiding researchers through methods and resources for this rapidly evolving field.

Keywords:
Commercial platformsSelection guideSpatial transcriptomicsTechnologies

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Spatial transcriptomics provides unprecedented insights into gene expression within tissue architecture.
  • The field has rapidly advanced with new technologies and data analysis methods.
  • Navigating the expanding landscape of spatial transcriptomics is challenging for researchers, particularly newcomers.

Purpose of the Study:

  • To provide an updated review of spatial transcriptomics technologies, with a focus on commercially available platforms.
  • To serve as a guiding resource for researchers, including newcomers, in selecting and utilizing spatial transcriptomics methods.
  • To equip researchers with knowledge on fundamental principles, data analysis challenges, experimental considerations, and available resources.

Main Methods:

  • Review of current and emerging spatial transcriptomics technologies.
  • Analysis of data processing and interpretation challenges.
  • Compilation of experimental considerations and available resources.
  • Development of a guide for method selection.

Main Results:

  • Identification of key principles underlying various spatial transcriptomic methods.
  • Discussion of common challenges in spatial transcriptomic data analysis.
  • Overview of experimental design considerations and practical resources.
  • A framework for selecting appropriate spatial transcriptomics technologies.

Conclusions:

  • Commercial spatial transcriptomics platforms offer accessible entry points for researchers.
  • Informed method selection is crucial for successful application of spatial transcriptomics.
  • This review aims to facilitate informed decision-making and advance research in spatial biology.