Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Lagging Strand Synthesis

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...

Lagging Strand Synthesis

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

Longitudinal Research

Longitudinal Research

Sometimes we want to see how people change over time, as in studies of human development and lifespan. When we test the same group of individuals repeatedly over an extended period of time, we are conducting longitudinal research. Longitudinal research is a research design in which data-gathering is administered repeatedly over an extended period of time. For example, we may survey a group of individuals about their dietary habits at age 20, retest them a decade later at age 30, and then again...

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

Qualitative Analysis

Qualitative Analysis

For solutions containing mixtures of different cations, the identity of each cation can be determined by qualitative analysis. This technique involves a series of selective precipitations with different chemical reagents, each reaction producing a characteristic precipitate for a specific group of cations. Metal ions within a group are further separated by varying the pH, heating the mixture to redissolve a precipitate, or adding other reagents to form complex ions.
For instance, group IV...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Pass/Fail Versus Tiered Grades and Academic Performance in Undergraduate Medical Education: Crossover Study.

JMIR medical education·2025

Same author

Differences in complement activation of serum-resistant and serum-sensitive Klebsiella pneumoniae isolates.

Molecular immunology·2025

Same author

A Comparative Analysis of the Wound Healing-Related Heterogeneity of Adipose-Derived Stem Cells Donors.

Pharmaceutics·2022

Same author

Support for mobilising medical students to join the COVID-19 pandemic emergency healthcare workforce: a cross-sectional questionnaire survey.

BMJ open·2020

Same author

Medical students for health-care staff shortages during the COVID-19 pandemic.

Lancet (London, England)·2020

Same author

Contention over undergraduate medical curriculum content.

International journal of medical education·2019

Search research articles

Related Experiment Video

Updated: Jul 7, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Duplicate ditag analysis in LongSAGE.

Jeppe Emmersen¹

¹Department of Biochemistry, Chemistry and Environmental Engineering, University of Aalborg, Aalborg, Denmark.

Methods in Molecular Biology (Clifton, N.J.)

|February 22, 2008

Summary

Duplicate ditags in Long Serial Analysis of Gene Expression (SAGE) can skew results. This chapter introduces a tool to analyze and manage these duplicate ditags in LongSAGE studies for accurate gene expression analysis.

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

The Long Serial Analysis of Gene Expression (SAGE) protocol is crucial for transcriptome analysis.
Overlapping overhangs in LongSAGE tag generation increase the likelihood of duplicate ditag formation.
Duplicate ditags can introduce biases in gene expression quantification.

Purpose of the Study:

To present a computational tool for analyzing duplicate ditags in LongSAGE data.
To provide a method for assessing the inclusion or exclusion of duplicate ditags.
To improve the accuracy of gene expression profiling from LongSAGE experiments.

Main Methods:

Development of a specialized software tool for duplicate ditag analysis.
Implementation of algorithms to identify and quantify duplicate ditags.

More Related Videos

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

Related Experiment Videos

Last Updated: Jul 7, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

Establishment of criteria for evaluating the significance of duplicate ditags.

Main Results:

The presented tool effectively identifies duplicate ditags in LongSAGE datasets.
The analysis provides a basis for informed decisions regarding duplicate ditag handling.
Demonstrated potential for reducing experimental bias in LongSAGE studies.

Conclusions:

Accurate management of duplicate ditags is essential for reliable LongSAGE results.
The developed tool offers a valuable resource for researchers using LongSAGE.
This approach enhances the integrity of gene expression data derived from LongSAGE.