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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 28, 2026

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
12:44

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in

Qichao Huang1, Biaoyang Lin, Hanqiang Liu

  • 1State Key Laboratory of Cancer Biology, Cell Engineering Research Center and Department of Cell Biology, Fourth Military Medical University, Xi'an, China.

Plos One
|November 2, 2011
PubMed
Summary

This study used RNA-sequencing to comprehensively analyze the transcriptome of Hepatitis B virus-related hepatocellular carcinoma (HCC). We identified numerous differentially expressed genes and exons, revealing complex molecular mechanisms and novel splicing variants in HCC.

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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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Last Updated: May 28, 2026

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
12:44

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

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

Published on: December 9, 2016

Area of Science:

  • Genomics
  • Molecular Biology
  • Oncology

Background:

  • Hepatocellular carcinoma (HCC) is a major global health concern, often linked to Hepatitis B virus (HBV) infection.
  • Comprehensive transcriptome analysis of HBV-related HCC using RNA-sequencing (RNA-seq) has not been previously reported.

Purpose of the Study:

  • To perform a detailed transcriptome analysis of HBV-related HCC using RNA-seq.
  • To identify differentially expressed genes (DEGs) and exons (DEEs) at both gene and exon levels.
  • To characterize novel splicing variants and understand the molecular mechanisms underlying HCC development.

Main Methods:

  • RNA-sequencing (RNA-seq) was performed on 10 matched pairs of HCC and non-cancerous tissues.
  • Solexa/Illumina GAII platform was used for sequencing, generating millions of reads per sample.
  • Bioinformatic analyses were conducted to identify DEGs, DEEs, and novel splicing events.

Main Results:

  • Over 50% of annotated genes were identified per sample.
  • 1,378 DEGs and 24,338 DEEs were identified.
  • Enrichment analyses revealed significant alterations in cell growth, metabolism, and immune pathways.
  • DEGs were notably enriched at chromosome 8q21.3-24.3.
  • Three distinct patterns of gene and exon expression changes were observed, indicating complex transcript-specific regulation.
  • A novel, highly upregulated exon-exon junction in the ATAD2 gene was identified in HCC tissues.

Conclusions:

  • This study provides the most comprehensive transcriptome characterization of HBV-related HCC to date.
  • RNA-seq revealed complex molecular mechanisms, including altered gene expression and novel splicing variants, contributing to HCC pathogenesis.
  • Findings offer critical insights into the molecular basis of HCC and highlight potential targets for future research.