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...

You might also read

Related Articles

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

Sort by

Same author

A striosomal accumbens pathway drives stereotyped behavior through an aversive Esr1+ hypothalamic-habenula circuit.

Science advances·2025

Same author

Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates.

Nature communications·2025

Same author

Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling.

Nature communications·2025

Same author

Identification of proliferating neural progenitors in the adult human hippocampus.

Science (New York, N.Y.)·2025

Same author

Efficient profiling of total RNA in single cells with STORM-seq.

bioRxiv : the preprint server for biology·2025

Same author

Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity.

Scientific reports·2025

Same journal

OmicsTransformer: Self-Supervised Masked Consistency and Uncertainty-Aware Fusion for Robust Multi-Omics Prediction.

Bioinformatics (Oxford, England)·2026

Same journal

Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection.

Bioinformatics (Oxford, England)·2026

Same journal

ARISE: RNA-Anchored Shared-Edge Topology and Hierarchical Fusion for Spatial Multi-Omics Integration.

Bioinformatics (Oxford, England)·2026

Same journal

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

Bioinformatics (Oxford, England)·2026

Same journal

PepMCP: A Graph-Based Membrane Contact Probability Predictor for Membrane-Lytic Antimicrobial Peptides.

Bioinformatics (Oxford, England)·2026

Same journal

ARGscape: A modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 16, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

scphaser: haplotype inference using single-cell RNA-seq data.

Daniel Edsgärd¹, Björn Reinius¹, Rickard Sandberg²

¹Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

Bioinformatics (Oxford, England)

|August 7, 2016

Summary

This summary is machine-generated.

scphaser, a new R package, reconstructs genetic haplotypes from single-cell RNA sequencing data. This method accurately phases alleles, improving the understanding of genetic variation

More Related Videos

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Published on: July 18, 2019

Chromatin Isolation by RNA Purification ChIRP

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

Related Experiment Videos

Last Updated: Mar 16, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Published on: July 18, 2019

Chromatin Isolation by RNA Purification ChIRP

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

Area of Science:

Genomics
Bioinformatics

Background:

Haplotype determination is crucial for understanding genetic variation's phenotypic effects in diploid organisms.
Allelic fluctuations in single-cell RNA sequencing (scRNA-seq) data offer potential for phasing genetic variants.

Purpose of the Study:

To introduce scphaser, an R package for reconstructing haplotypes from scRNA-seq data.
To leverage allelic fluctuations in scRNA-seq for accurate variant phasing.

Main Methods:

scphaser utilizes scRNA-seq data to phase alleles at heterozygous variants.
The method reconstructs haplotypes within transcribed genomic regions.

Main Results:

scphaser accurately reconstructed known haplotypes for over 93% of phasable genes in human and mouse.
The tool enables phasing of rare, de novo, and distant variants, overcoming limitations of population-based methods.

Conclusions:

scphaser provides an efficient and accurate method for haplotype reconstruction using scRNA-seq.
This approach enhances the study of genetic variation, including cis-regulatory control and compound heterozygosity.