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

RNA-seq

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...

You might also read

Related Articles

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

Sort by

Same author

MIC-Drop-seq: scalable single-cell phenotyping of mutant vertebrate embryos.

Nature communications·2026

Same author

ModSeqR: an R package for efficient analysis of modified nucleotide data.

BMC genomics·2026

Same author

Nuclear Histone 3 Post-Translational Modification Profiling in Whole Cells using Spectral Flow Cytometry.

bioRxiv : the preprint server for biology·2026

Same author

Functional divergence of Tbx2a and Tbx2b in zebrafish heart development.

EvoDevo·2025

Same author

An Integrated Investigation of SOX10 in Feather Color in Domestic Rock Pigeon (Columba livia).

Pigment cell & melanoma research·2025

Same author

Genome sequencing is critical for forecasting outcomes following congenital cardiac surgery.

Nature communications·2025

Same journal

Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.

Genome research·2026

Same journal

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution.

Genome research·2026

Same journal

A unified analysis of cell type- and trajectory-associated pathways in single-cell data using Phoenix.

Genome research·2026

Same journal

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin.

Genome research·2026

Same journal

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.

Genome research·2026

Same journal

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD.

Genome research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 15, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.

Jonathon T Hill¹, Bradley L Demarest, Brent W Bisgrove

¹Department of Neurobiology and Anatomy, University of Utah Molecular Medicine Program, University of Utah, Salt Lake City, Utah 84112, USA.

Genome Research

|January 10, 2013

Summary

This summary is machine-generated.

We developed a Mutation Mapping Analysis Pipeline for Pooled RNA-seq (MMAPPR) to efficiently map mutations in model organisms. This automated tool accelerates genetic discovery without parental strains or SNP maps.

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Related Experiment Videos

Last Updated: May 15, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Area of Science:

Genetics
Developmental Biology
Genomics

Background:

Forward genetic screens identify essential genes but mutation mapping is labor-intensive.
Existing mapping methods often require parental strains or pre-existing SNP maps, limiting their applicability.
High-throughput sequencing offers potential for improved mutation mapping.

Purpose of the Study:

To develop a rapid, cost-efficient, and automated pipeline for mutation mapping using pooled RNA-sequencing data.
To create a tool that does not require parental strain information or a pre-existing SNP map.
To adapt mutation mapping to organisms with differential recombination frequencies and noisy RNA-seq data.

Main Methods:

Developed the Mutation Mapping Analysis Pipeline for Pooled RNA-seq (MMAPPR).
MMAPPR calculates allelic frequency using Euclidean distance and Loess regression.
Identifies mutation location and lists putative coding region mutations within the linked genomic segment.

Main Results:

MMAPPR successfully mapped mutations in known zebrafish lines (nkx2.5, tbx1).
Identified novel cardiovascular mutants with mutations in ctr9 and cds2 genes.
Demonstrated applicability to various model organisms like zebrafish, Drosophila, and C. elegans.

Conclusions:

MMAPPR is a versatile, automated pipeline for efficient mutation mapping in diverse model organisms.
The pipeline accommodates RNA-seq noise and variable recombination frequencies.
Enables rapid genetic discovery for developmental and disease processes.