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Related Concept Videos

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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.
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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. 
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Related Experiment Video

Updated: Jul 30, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler.

Nan Wang1, Xia Li1, Zhiyong Ding2

  • 1Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan City, Shandong Province, P. R. China.

Methods in Molecular Biology (Clifton, N.J.)
|May 16, 2023
PubMed
Summary

This study provides a detailed protocol and practical tips for using the Digital Spatial Profiler (DSP). Optimize your spatial transcriptomics and proteomics experiments with these expert insights.

Keywords:
Cancer Transcriptome Atlas (CTA)Companion diagnostics (CDs)Digital Spatial Profiler (DSP), Whole Transcriptome Atlas (WTA)Next-generation sequencing (NGS)-based barcodeSpatial biology, Transcriptomics, Proteomics, Formalin-fixed paraffin-embedded (FFPE) specimens

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Area of Science:

  • Biomedical Research
  • Molecular Biology
  • Genomics

Background:

  • Spatial multi-omics technologies are revolutionizing biomedical research.
  • The Digital Spatial Profiler (DSP) is a leading platform for spatial transcriptomics and proteomics.
  • DSP aids in understanding complex biological systems.

Purpose of the Study:

  • To provide a comprehensive, hands-on protocol for the Digital Spatial Profiler (DSP).
  • To share practical handling notes based on three years of experience with DSP.
  • To enable the broader scientific community to optimize their DSP workflows.

Main Methods:

  • Detailed protocol development for DSP experiments.
  • Inclusion of key practical handling notes and optimization strategies.
  • Focus on spatial transcriptomics and proteomics applications.

Main Results:

  • A validated, step-by-step protocol for DSP implementation.
  • Identification of critical parameters and potential pitfalls for successful experiments.
  • Guidelines for optimizing data acquisition and analysis.

Conclusions:

  • The provided protocol and notes will enhance the usability and efficiency of DSP.
  • This resource empowers researchers to effectively utilize DSP for spatial multi-omics studies.
  • Facilitates deeper insights into complex biological questions using spatial profiling.