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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...

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Updated: Sep 4, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq.

Silke J A Lochs¹, Jop Kind²

¹Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Radboud University & Oncode Institute, Utrecht, The Netherlands.

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

|July 22, 2022

Summary

We developed scDam&T-seq, a new method to simultaneously measure protein-DNA interactions and gene expression in single cells. This tool helps understand how genome organization impacts gene activity.

Keywords:

CEL-Seq2 DamID Lamina-associated domains Protein–DNA interactions Single-cell genomics

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Last Updated: Sep 4, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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Published on: March 12, 2021

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Published on: January 10, 2019

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Published on: January 7, 2020

Area of Science:

Molecular Biology
Genomics
Cell Biology

Background:

Spatial genome organization is crucial for gene expression and cell differentiation in mammals.
The direct impact of genome organization on gene expression remains unclear.
Existing methods lack the ability to simultaneously assess protein-DNA interactions and transcriptomes at a single-cell level.

Purpose of the Study:

To develop a novel single-cell method for simultaneously quantifying protein-DNA interactions and transcriptomes.
To investigate the direct relationship between spatial genome organization and gene expression.
To provide a versatile tool for studying various protein-DNA interactions and their effects on gene expression.

Main Methods:

Developed scDam&T-seq, integrating DamID for protein-DNA contact measurement and CEL-Seq2 for single-cell transcriptome quantification.
Applied scDam&T-seq to study DNA contacts with the nuclear lamina.
Simultaneously measured protein-DNA interactions and gene expression profiles in individual cells.

Main Results:

Successfully implemented scDam&T-seq for simultaneous measurement of protein-DNA contacts and transcriptomes.
Demonstrated the method's ability to link DNA contacts, such as those with the nuclear lamina, to specific gene expression patterns.
Provided insights into how spatial genome organization influences gene activity at a single-cell resolution.

Conclusions:

scDam&T-seq is an effective method for dissecting the relationship between spatial genome organization and gene expression.
The developed technique offers a powerful approach to study diverse protein-DNA interactions and their functional consequences.
This method advances our understanding of gene regulation within the context of genome architecture.