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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. 
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
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Related Experiment Video

Updated: Aug 9, 2025

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets
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Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

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Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA).

Courtney Schiebout1, Hannah E Lust2, Yina H Huang3

  • 1Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH USA.

Biorxiv : the Preprint Server for Biology
|February 24, 2023
PubMed
Summary
This summary is machine-generated.

Biological doublets in single-cell RNA sequencing (scRNA-seq) can reveal cell interactions. Our new pipeline, CIcADA, identifies these doublets to analyze immune cell juxtacrine interactions in tumors.

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Area of Science:

  • Single-cell genomics
  • Computational biology
  • Immunology

Background:

  • Single-cell RNA sequencing (scRNA-seq) typically treats doublets as artifacts for removal.
  • However, doublets can represent genuine cell-cell interactions, particularly juxtacrine interactions, offering valuable biological insights.
  • Tumor microenvironment immune cell interactions are critical prognostic indicators.

Approach:

  • Developed Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA) pipeline.
  • CIcADA identifies biological doublets using multi-label cell type scores.
  • Analyzes doublet interactions by comparing them to computationally generated synthetic doublets.

Key Points:

  • CIcADA successfully identified biological doublets in scRNA-seq tumor datasets.
  • Identified doublets consistently showed upregulation of immune response genes.
  • This suggests doublets can serve as a proxy for studying cell-cell communication.

Conclusions:

  • Biological doublets, when analyzed correctly, provide meaningful data on cell interactions.
  • CIcADA offers a novel method for leveraging doublets to understand tissue microenvironments.
  • This approach has implications for cancer immunology and biomarker discovery.