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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...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: Jun 1, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.

Oguzhan Begik1, Gregor Diensthuber1,2, Ivana Borovska3

  • 1Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

Genome Biology
|May 30, 2026
PubMed
Summary
This summary is machine-generated.

FIRST-seq is a new nanopore sequencing method for mapping RNA modifications. It accurately detects modifications like m1A and m3C, revealing RNA structures in vitro and in vivo.

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AQRNA-seq for Quantifying Small RNAs
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Related Experiment Videos

Last Updated: Jun 1, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing
06:57

Enrichment of mRNA and Bisulfite-mRNA Library Preparation for Next-Generation Sequencing

Published on: July 7, 2023

AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA modifications are crucial for cellular function and gene regulation.
  • Existing methods for RNA modification detection have limitations in resolution, cost, or enzyme compatibility.
  • Reverse transcription (RT) errors can be leveraged to map RNA modifications.

Purpose of the Study:

  • To develop a flexible, cost-effective nanopore cDNA sequencing method for RNA modification detection.
  • To enable single-nucleotide resolution analysis of RT signatures for various RNA modifications.
  • To optimize conditions for accurate RNA modification profiling using long-read sequencing.

Main Methods:

  • Developed FIRST-seq, a nanopore cDNA method avoiding second-strand synthesis and PCR.
  • Benchmarked multiple reverse transcription (RT) enzymes and buffers to optimize error detection and minimize premature termination.
  • Integrated FIRST-seq with Dimethyl sulfate (DMS) probing for detecting specific RNA modifications.

Main Results:

  • Identified optimal RT enzymes and buffers for enhanced error detection and reduced premature termination.
  • Demonstrated FIRST-seq's ability to accurately detect m1A and m3C modifications at unpaired sites.
  • Successfully recapitulated known RNA structures in vitro and in vivo using FIRST-seq coupled with DMS probing.

Conclusions:

  • FIRST-seq is a versatile and cost-effective platform for profiling RNA modifications using long-read sequencing.
  • The method enables accurate detection of chemical-induced and natural RNA modifications.
  • FIRST-seq facilitates the study of RNA structure and function through precise modification mapping.