Related Concept Videos
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
03:00Next-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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:24Ribosome 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...
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...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
01:30General Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
01:44Complementary DNA
Overview
You might also read
Related Articles
Articles linked to this work by shared authors, journal, and citation graph.
Sort by
Same author
HGVS Nomenclature 2024: improvements to community engagement, usability, and computability.
Genome medicine·2024
Same author
Comparison of the ABC and ACMG systems for variant classification.
European journal of human genetics : EJHG·2024
Same author
Systematic large-scale application of ClinGen InSiGHT <i>APC</i> -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases.
medRxiv : the preprint server for health sciences·2024
Same author
Hematologically important mutations: Leukocyte adhesion deficiency (second update).
Blood cells, molecules & diseases·2023
Same author
Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene (<i>DMD</i>).
International journal of molecular sciences·2022
Same journal
VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.
Nucleic acids research·2026
Same journal
Accessibility of telomeric overhangs to stabilizing small-molecule ligands.
Nucleic acids research·2026
Same journal
Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.
Nucleic acids research·2026
Same journal
Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.
Nucleic acids research·2026
Same journal
Epigenetic landscape of synthetic human centromere core regions: CENP-A assembly and euchromatic modifications interdependently antagonize heterochromatin accumulation.
Nucleic acids research·2026
Same journal
MAPK/ERK signaling regulates H3K9me3 heterochromatin reorganization to confer mesendoderm developmental competence.
Nucleic acids research·2026
Related Experiment Video
Updated: Jun 11, 2026
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing
Matthew S Hestand1, Andreas Klingenhoff, Matthias Scherf
1The Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.
Nucleic Acids Research
|July 10, 2010
Summary
Comparing cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE) for gene expression studies, both methods showed high reproducibility and identified thousands of differentially expressed genes in myogenesis. These techniques enhance genome annotation with promoter and 3'-UTR data.
Area of Science:
- Molecular Biology
- Genomics
- Transcriptomics
Background:
- Next-generation sequencing (NGS) is a powerful tool for quantifying mRNA abundance and studying gene expression.
- Cap analysis of gene expression (CAGE) identifies transcription start sites, while serial analysis of gene expression (SAGE) monitors 3 e-end usage.
- Understanding transcriptional control in myogenesis requires accurate gene expression profiling.
Purpose of the Study:
- To compare the performance of CAGE and SAGE for gene expression analysis using the same RNA samples.
- To investigate the transcriptional control of myogenesis by studying differential gene expression in C2C12 myoblasts.
- To evaluate the reproducibility and differential gene expression findings from both CAGE and SAGE.
Main Methods:
- Utilized cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE) on identical RNA samples from C2C12 myoblasts.
- Performed differential gene expression analysis between proliferating and differentiated C2C12 myoblast states.
- Conducted statistical evaluation for reproducibility and differential gene expression accuracy.
Main Results:
- Both CAGE and SAGE demonstrated high reproducibility (Pearson's correlations >0.92) across biological triplicates.
- Approximately 10,000 genes were found to be expressed above 2 transcripts per million with 86% overlap between methods.
- Identified 4304 (CAGE) and 3846 (SAGE) differentially expressed genes, with 2144 overlapping, and discovered 196 novel regulatory regions.
Conclusions:
- NGS-based CAGE and SAGE provide consistent and reliable gene expression quantification.
- These methods can significantly enrich genome annotations by identifying tissue-specific promoters and alternative 3 e-UTR usage.
- CAGE and SAGE are valuable complementary techniques for comprehensive transcriptomic analysis, particularly in studying complex biological processes like myogenesis.