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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: May 6, 2026

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

Massively multiplex chemical transcriptomics at single-cell resolution.

Sanjay R Srivatsan^1,2, José L McFaline-Figueroa¹, Vijay Ramani^1,3

¹Department of Genome Sciences, University of Washington, Seattle, WA, USA.

Science (New York, N.Y.)

|December 7, 2019

Summary

This summary is machine-generated.

We developed sci-Plex, a method using nuclear hashing to analyze single-cell transcriptional responses to thousands of chemical compounds. This approach reveals detailed cellular responses and compound family similarities, advancing drug screening capabilities.

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Last Updated: May 6, 2026

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

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

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

Area of Science:

Single-cell genomics
Chemical biology
Drug discovery

Background:

Traditional high-throughput chemical screens offer limited insights into drug mechanisms and cellular responses.
Understanding heterogeneous cellular responses to compounds is crucial for effective drug development.

Purpose of the Study:

To introduce sci-Plex, a novel method for high-resolution analysis of transcriptional responses to chemical perturbations.
To demonstrate the capability of sci-Plex in profiling large-scale single-cell transcriptomic data.

Main Methods:

Development and application of sci-Plex, utilizing nuclear hashing for single-cell RNA sequencing.
Screening of three cancer cell lines against 188 compounds, generating ~650,000 single-cell transcriptomes.
Analysis of transcriptional profiles to identify compound-specific and family-related cellular responses.

Main Results:

Sci-Plex enabled the profiling of ~5000 independent samples in a single experiment at single-cell resolution.
Identified significant intercellular heterogeneity in cellular responses to individual compounds.
Revealed commonalities in responses to compound families and differential effects within families.

Conclusions:

Sci-Plex offers a powerful platform for dissecting complex cellular responses to chemical perturbations at unprecedented scale and resolution.
The findings provide new insights into drug mechanisms, off-target effects, and personalized medicine.
Results with histone deacetylase inhibitors suggest chromatin's role as an acetate reservoir in cancer cells.