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Related Concept Videos

RNA-seq03:21

RNA-seq

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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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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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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Related Experiment Video

Updated: Jan 11, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq.

Anna K Casasent1, Danielle L Stolley1, Basant T Gamal2

  • 1Department of Hematopoietic Biology and Malignancies, The University of Texas MD Anderson Cancer Center.

Journal of Visualized Experiments : Jove
|November 17, 2025
PubMed
Summary

This study introduces a novel spatial species-agnostic Stereo-seq protocol for formalin-fixed paraffin-embedded (FFPE) tissues. It enables subcellular resolution detection of diverse RNA species, including microbial and viral RNA, within their spatial context.

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Area of Science:

  • Spatial transcriptomics
  • Molecular biology
  • Genomics

Background:

  • Cellular spatial composition and microbial loads influence host-tissue interactions.
  • Existing spatial transcriptomics methods often miss non-messenger RNA (mRNA) species like long non-coding RNA, mitochondrial RNA, and microbial RNA.
  • Formalin-fixed paraffin-embedded (FFPE) tissues are valuable but challenging for comprehensive spatial RNA analysis.

Purpose of the Study:

  • To present a detailed protocol for spatial species-agnostic Stereo-seq on FFPE tissues.
  • To enable detection of a wide range of RNA species, including host and non-host RNA, with subcellular resolution.
  • To provide insights into the spatial distribution of diverse RNA molecules within tissues.

Main Methods:

  • Utilizes a random priming approach with spatial barcodes for RNA capture in FFPE tissues.
  • Employs a randomer probe methodology for species-agnostic RNA detection.
  • Incorporates specific considerations for distinguishing endogenous RNA from environmental contaminants during sample processing.

Main Results:

  • Achieves subcellular resolution (0.22 µm beads, 0.5 µm array) for spatial RNA detection.
  • Successfully detects both host and non-host RNA (microbial, viral) within FFPE tissues.
  • Provides high-resolution spatial mapping of multiple RNA species, including single-cell level resolution.

Conclusions:

  • The developed spatial Stereo-seq protocol is compatible with FFPE tissues and offers broad RNA species detection.
  • This method enhances understanding of host-microbe and host-pathogen interactions in a spatial context.
  • It offers significant potential for studying complex tissue microenvironments and disease pathology.