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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...

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Related Experiment Video

Updated: Jul 1, 2026

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
11:42

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Published on: October 27, 2017

Advancing Functional Transcriptomics in Zebrafish with High-accuracy Full-length RNA Sequencing.

Monika Kwiatkowska1, Tomasz Mądry1, Marta Blangiewicz1

  • 1Department of Computational Biology of Non-coding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.

Genomics, Proteomics & Bioinformatics
|June 30, 2026
PubMed
Summary
This summary is machine-generated.

CapTrap-seq enhances zebrafish transcriptomics by capturing full-length RNA, improving gene discovery and isoform resolution. This method offers a robust framework for studying complex transcriptomes in under-annotated species.

Keywords:
Danio rerioFull-length sequencingGenome annotationLong-read RNA sequencingZebrafish

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Last Updated: Jul 1, 2026

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
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Mosaic Zebrafish Transgenesis for Evaluating Enhancer Sequences

Published on: July 16, 2010

Area of Science:

  • * Genomics
  • * Molecular Biology
  • * Developmental Biology

Background:

  • * Zebrafish (Danio rerio) is a key vertebrate model organism with human genetic and physiological similarities.
  • * Current transcriptomic research in zebrafish is limited by incomplete gene annotations and inefficient methods.
  • * Need for high-resolution transcript-level analysis in zebrafish for functional genomics.

Purpose of the Study:

  • * To apply CapTrap-seq, a long-read RNA sequencing method, to zebrafish developmental stages and adult tissues.
  • * To improve the capture of full-length transcripts and enhance transcriptomic resolution.
  • * To benchmark CapTrap-seq against existing methods like template-switching oligo (TSO) and assess its performance in a non-mammalian system.

Main Methods:

  • * Utilized CapTrap-seq, a platform-agnostic approach combining cap-trapping with oligo(dT) priming for selective capture of 5'-capped, full-length transcripts.
  • * Incorporated a size-selection step to improve recovery of longer RNA molecules.
  • * Applied the method to zebrafish developmental stages and adult tissues, comparing results with existing long-read catalogues.

Main Results:

  • * CapTrap-seq enabled accurate and reproducible transcript reconstruction in zebrafish without external ribodepletion or validation.
  • * Detected a greater number of biologically relevant genes, including oxidative phosphorylation, cardiac, and OMIM disease genes.
  • * Revealed extensive novel isoform diversity and resolved complex splicing landscapes in lncRNA loci, uncovering new full-length isoforms.

Conclusions:

  • * CapTrap-seq provides a robust, genome-agnostic framework for high-quality transcriptome characterization in zebrafish.
  • * The method overcomes limitations of incomplete annotations and improves transcript-level resolution.
  • * Offers significant implications for functional genomics and translational research in zebrafish and other under-annotated species.