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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...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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...
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 15, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Poly(A)+ selection limits detection of long and alternatively spliced transcripts compared with rRNA depletion in

Swethaa Natraj Gayathri1,2, Victoria Lillback3,4, Bjarne Udd4

  • 1University of Helsinki, Helsinki, Finland. swethaa.natrajgayathri@helsinki.fi.

BMC Genomics
|May 14, 2026
PubMed
Summary

Ribosomal RNA depletion in RNA sequencing offers better transcript detection and coverage than poly(A)+ selection, especially for long RNA molecules. This method is crucial for studying complex transcriptomes in basic biology and precision medicine.

Keywords:
MusclePoly(A)+RNA-SequencingTTNTranscriptomicsrRNA

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

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Last Updated: May 15, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Alternative splicing drives eukaryotic transcriptome diversity.
  • RNA sequencing is vital for gene expression, alternative splicing, and pathway analysis in biology and medicine.
  • Non-ribosomal RNAs comprise 20% of cellular RNA, necessitating diverse library preparation methods.

Purpose of the Study:

  • To compare poly(A)+ selection and ribosomal RNA (rRNA) depletion RNA sequencing library preparation techniques.
  • To evaluate their impact on transcript representation, coverage, and splice junction detection.
  • To highlight the importance of choosing appropriate methods for different research contexts.

Main Methods:

  • Analysis of blood and skeletal muscle transcriptomics datasets.
  • Comparison of poly(A)+ selected RNA-Seq and rRNA-depleted RNA-Seq libraries.
  • Assessment of transcript representation, 5'-3' coverage, and splice junction detection.

Main Results:

  • Poly(A)+ selection showed length-dependent biases, reduced splice junction detection, and 3' coverage bias for transcripts >5 kb.
  • rRNA depletion provided more uniform 5'-3' coverage and improved splice junction detection.
  • rRNA depletion robustly detected extremely large transcripts (e.g., OBSCN, TTN).

Conclusions:

  • RNA-Seq library preparation methods differentially capture RNA types.
  • rRNA depletion is superior for detecting long transcripts and offers more uniform coverage.
  • Selecting the appropriate RNA-Seq library preparation is critical for accurate biological and clinical interpretation.