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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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Related Experiment Video

Updated: Jun 4, 2025

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma

Published on: June 10, 2017

HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling.

Jan Otoničar^1,2,3, Olga Lazareva^4,5,6, Jan-Philipp Mallm^7,8

¹Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.

|December 19, 2024

Summary

We developed HIPSD&R-seq, a scalable assay for high-throughput single-cell DNA and RNA sequencing. This method efficiently detects rare cancer clones by profiling thousands of cells simultaneously.

Keywords:

Single Cell DNA sequencing Single Cell copy Number profiling Single Cell multiome

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Last Updated: Jun 4, 2025

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma

Published on: June 10, 2017

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Area of Science:

Genomics
Molecular Biology
Cancer Research

Background:

Single-cell DNA sequencing (scDNA-seq) is crucial for understanding somatic cancer variation.
Current scDNA-seq methods face limitations in throughput and integration with transcriptome sequencing.
A need exists for scalable, accessible assays to profile both DNA and RNA at the single-cell level.

Purpose of the Study:

To introduce HIPSD&R-seq (HIgh-throughPut Single-cell Dna and Rna-seq), a novel assay for parallel low-coverage DNA and RNA profiling.
To demonstrate the scalability and accessibility of the HIPSD&R-seq assay.
To validate the assay's capability in detecting rare cell populations.

Main Methods:

Modification of the 10X Genomics platform for simultaneous scATAC and multiome profiling.
Development of a high-throughput assay for low-coverage DNA and RNA sequencing in single cells.
Application of combinatorial indexing to achieve large-scale cell profiling.

Main Results:

HIPSD&R-seq successfully profiles low-coverage DNA and RNA in thousands of cells in parallel.
The assay demonstrated feasibility in human cell models and primary tissues.
Rare clones were effectively detected using the HIPSD&R-seq method.
Combinatorial indexing enabled profiling of over 17,000 cells.

Conclusions:

HIPSD&R-seq offers a scalable, simple, and accessible solution for single-cell DNA and RNA sequencing.
The assay enables the detection of rare clones, advancing cancer genomics research.
HIPSD&R-seq integrates DNA and RNA profiling, providing comprehensive single-cell insights.