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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: May 9, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Protocol for analyzing tRNA-derived ncRNAs from small RNA-seq data using tRFUniverse functional analyses.

Alessandro La Ferlita1, Giovanni Nigita2, Alfredo Ferro3

  • 1Department of Internal Medicine, Division of Medical Oncology, Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.

STAR Protocols
|June 12, 2025
PubMed
Summary
This summary is machine-generated.

This study presents a protocol for analyzing tRNA-derived fragments (tRFs) using small RNA sequencing (smRNA-seq). The method helps identify dysregulated tRFs in diseases like lung cancer.

Keywords:
BioinformaticsCancerGenomicsRNAseqSequence analysis

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Last Updated: May 9, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

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Published on: May 9, 2017

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Published on: May 28, 2021

AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Small RNA sequencing (smRNA-seq) is crucial for understanding tRNA-derived fragments (tRFs).
  • tRFs play significant roles in human physiology and disease.
  • Standardized protocols are needed for accurate tRF expression analysis.

Purpose of the Study:

  • To present a comprehensive protocol for assessing tRF expression from smRNA-seq data.
  • To enable robust quantification and harmonization of tRF expression data.
  • To facilitate functional analysis of tRFs in disease contexts.

Main Methods:

  • Detailed steps for smRNA-seq data preprocessing, including quality filtering and adapter trimming.
  • Read mapping strategies for accurate tRF identification.
  • Procedures for quantifying tRF expression and harmonizing datasets.
  • Utilizing tRFUniverse for functional analysis.

Main Results:

  • The protocol effectively assesses tRF expression from smRNA-seq data.
  • Lung cancer case study using TCGA data revealed significantly dysregulated tRFs.
  • Identified specific tRFs implicated in the pathogenesis of lung cancer.

Conclusions:

  • The developed protocol provides a reliable method for tRF expression analysis.
  • Dysregulated tRFs are potential biomarkers and therapeutic targets in lung cancer.
  • This work facilitates further research into tRFs in human health and disease.