Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq

Samuel H Kim; Georgi K Marinov; S Tansu Bagdatli; Soon Il Higashino; Zohar Shipony; Anshul Kundaje; William J Greenleaf

doi:10.1007/978-1-0716-2899-7_11

Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq

Methods Mol Biol. 2023:2611:187-230. doi: 10.1007/978-1-0716-2899-7_11.

Authors

Samuel H Kim^{1

2}, Georgi K Marinov³, S Tansu Bagdatli³, Soon Il Higashino³, Zohar Shipony³, Anshul Kundaje^{3

4}, William J Greenleaf^{3

5

6

7}

Affiliations

¹ Cancer Biology Program, School of Medicine, Stanford University, Stanford, CA, USA. samhkim@stanford.edu.
² Medical Scientist Training Program, Stanford University, Stanford, CA, USA. samhkim@stanford.edu.
³ Department of Genetics, Stanford University, Stanford, CA, USA.
⁴ Department of Computer Science, Stanford University, Stanford, CA, USA.
⁵ Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
⁶ Department of Applied Physics, Stanford University, Stanford, CA, USA.
⁷ Chan Zuckerberg Biohub, San Francisco, CA, USA.

PMID: 36807070
DOI: 10.1007/978-1-0716-2899-7_11

Abstract

The ability to analyze the transcriptomic and epigenomic states of individual single cells has in recent years transformed our ability to measure and understand biological processes. Recent advancements have focused on increasing sensitivity and throughput to provide richer and deeper biological insights at the cellular level. The next frontier is the development of multiomic methods capable of analyzing multiple features from the same cell, such as the simultaneous measurement of the transcriptome and the chromatin accessibility of candidate regulatory elements. In this chapter, we discuss and describe SHARE-seq (Simultaneous high-throughput ATAC, and RNA expression with sequencing) for carrying out simultaneous chromatin accessibility and transcriptome measurements in single cells, together with the experimental and analytical considerations for achieving optimal results.

Keywords: Chromatin accessibility; Multiomics; Split–pool; Transcriptomics; scATAC-seq; scRNA-seq.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Chromatin*
High-Throughput Nucleotide Sequencing / methods
Regulatory Sequences, Nucleic Acid
Sequence Analysis, DNA / methods
Single-Cell Analysis / methods
Transcriptome*

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding