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Related Concept Videos

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...
Small interfering RNAs (siRNA)02:30

Small interfering RNAs (siRNA)

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...

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Updated: May 28, 2026

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

A bias-reducing strategy in profiling small RNAs using Solexa.

Guihua Sun1, Xiwei Wu, Jinhui Wang

  • 1Department of Molecular Pharmacology, Beckman Research Institute of the City of Hope, Duarte, California 91010-3000, USA.

RNA (New York, N.Y.)
|October 22, 2011
PubMed
Summary
This summary is machine-generated.

Customized adaptors in small RNA sequencing minimize bias. Using pooled adaptors reveals the true small RNAome composition, improving accuracy in next-generation sequencing studies.

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Last Updated: May 28, 2026

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
08:49

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Small RNAs (smRNAs) are crucial noncoding RNAs with diverse functions.
  • Advancements in detection techniques, particularly next-generation sequencing (NGS), have driven smRNA research.
  • NGS offers high-throughput and digitized smRNA profiling but can be subject to biases.

Purpose of the Study:

  • To identify and address biases in small RNA profiling using Solexa technology.
  • To develop a method for optimizing smRNA profiling accuracy.
  • To reveal the true composition of the small RNAome.

Main Methods:

  • Small RNA profiling using Solexa deep-sequencing technology.
  • Systematic analysis of biases introduced by 5' adaptors.
  • Development and testing of customized adaptor pooling strategies.

Main Results:

  • Significant biases in small RNA species coverage and abundance were observed due to 5' adaptors.
  • A pool of 64 customized 5' adaptors significantly optimized profiling results.
  • Reducing the pool to four smaller index pools (16 adaptors each) further minimized bias and facilitated multiplexing.

Conclusions:

  • The 5' adaptor sequences are a major source of bias in smRNA deep sequencing.
  • Customized adaptor pooling is an effective strategy to mitigate bias and improve the accuracy of smRNA profiling.
  • This adaptor pooling approach is a potential workaround for other deep-sequencing technologies to uncover the "true" small RNAome.