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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...
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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.
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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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Related Experiment Video

Updated: May 27, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro

Ru Huang1, Markus Jaritz, Philipp Guenzl

  • 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Plos One
|November 22, 2011
PubMed
Summary

This study optimized RNA sequencing to detect long non-coding RNAs (lncRNAs) in mouse tissues. The improved method accurately captures full-length imprinted lncRNAs, enhancing transcriptome analysis reproducibility.

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AQRNA-seq for Quantifying Small RNAs
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Last Updated: May 27, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Published on: August 4, 2016

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
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AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Imprinted macro non-protein-coding RNAs (ncRNAs) are crucial cis-repressors regulating multiple genes within imprinted gene clusters.
  • Long ncRNAs are prevalent in the mammalian genome, but their full-length characterization remains challenging.

Purpose of the Study:

  • To present an optimized RNA sequencing (RNA-Seq) strategy for comprehensive transcriptome analysis.
  • To accurately detect and characterize full-length imprinted macro ncRNAs.
  • To improve the reproducibility and comparability of transcriptome data.

Main Methods:

  • Utilized an optimized RNA-Seq strategy on two mouse tissues: differentiated embryonic stem (ES) cells and fetal head.
  • Employed RNA hydrolysis for RNA fragmentation, comparing it with cDNA fragmentation by shearing.
  • Analyzed transcript read coverage and length distribution.

Main Results:

  • The optimized RNA-Seq strategy demonstrated high reproducibility across different sequencing locations.
  • Successfully detected the full length of imprinted macro ncRNAs (e.g., Airn, Kcnq1ot1) ranging from 80-118 kb.
  • RNA hydrolysis resulted in more uniform read coverage compared to cDNA shearing, although transcripts >8 kb showed 3' end tag loss regardless of method.

Conclusions:

  • The presented RNA-Seq strategy is more efficient for detecting functional imprinted macro ncRNAs.
  • Standardization of RNA preparation protocols is recommended to enhance transcriptome data comparability across studies.
  • This work provides a robust method for characterizing long ncRNAs, crucial for understanding gene regulation.