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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: Jul 8, 2025

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

Published on: March 23, 2022

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

Andrew J C Russell^1,2, Jackson A Weir^1,3, Naeem M Nadaf¹

¹Broad Institute of Harvard and MIT, Cambridge, MA, USA.

|December 13, 2023

Summary

This summary is machine-generated.

Slide-tags technology enables precise spatial mapping of individual cells within intact tissues. This innovation integrates seamlessly with existing single-cell assays, advancing spatial genomics and tissue analysis.

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Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

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Published on: April 7, 2023

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Published on: April 14, 2015

Related Experiment Videos

Last Updated: Jul 8, 2025

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

Published on: March 23, 2022

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Published on: April 14, 2015

Area of Science:

Genomics
Molecular Biology
Biotechnology

Background:

High-throughput single-cell technologies have revolutionized tissue biology but lack routine spatial localization.
Precisely mapping cells in tissues is crucial for understanding complex biological systems.

Purpose of the Study:

To develop a versatile method for spatially localizing profiled cells within intact tissues.
To integrate spatial information with various single-cell omics measurements.

Main Methods:

Developed Slide-tags: a strategy to tag single nuclei in intact tissue sections with spatial barcodes.
Applied Slide-tags to mouse hippocampus, human brain, tonsil, and melanoma tissues.
Performed multiomic measurements including RNA, open chromatin, and T cell receptor sequences.

Main Results:

Achieved sub-10 micrometer spatial resolution in mouse hippocampus with high-quality whole-transcriptome data.
Revealed cell-type-specific gene expression patterns and spatially contextualized receptor-ligand interactions in human tissues.
Identified transcription factor motifs driving cancer cell transitions in distinct melanoma microenvironments.

Conclusions:

Slide-tags provides a universal platform for spatial genomics, adaptable to diverse single-cell assays.
Enables the integration of established single-cell measurements into the spatial domain.
Advances the study of tissue architecture and cellular interactions in health and disease.