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Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution.

Emily Lauren Sylwestrak¹, Priyamvada Rajasethupathy¹, Matthew Arnot Wright²

¹Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.

|February 13, 2016

Summary

This study introduces a novel method for labeling nucleic acids within intact tissues, overcoming limitations of protein-based methods. This advance enables comprehensive molecular phenotyping for broader scientific and clinical applications.

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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

Area of Science:

Molecular biology
Biotechnology
Genomics

Background:

Current high-resolution tissue imaging is limited to protein labeling.
Volumetric nucleic acid labeling offers greater potential for RNA variant and non-coding RNA detection.
Antibody-based methods for large tissue volumes face cost, availability, and multiplexing limitations.

Purpose of the Study:

To develop a versatile, high-content, and scalable method for molecular phenotyping of intact tissues.
To enable robust detection of various RNA species in large tissue volumes.
To overcome limitations of current protein-based imaging techniques.

Main Methods:

Developed a carbodiimide-based chemistry for stable RNA retention in clarified tissues.
Utilized amplification tools for multiplexed detection of labeled nucleic acids.
Applied the method to rodent and human tissue volumes.

Main Results:

Successfully enabled stable retention and multiplexed detection of RNAs in clarified tissues.
Demonstrated robust measurement of transcriptional signatures, cell-identity markers, and non-coding RNAs.
Validated the method across both rodent and human tissue samples.

Conclusions:

The carbodiimide-based chemistry provides a scalable solution for volumetric nucleic acid labeling in intact tissues.
This technology facilitates high-content molecular phenotyping, expanding research possibilities.
An online resource of validated probes is established to foster community development.