Single-Cell Analysis of circRNA Using ddPCR

Jiayi Peng; Feng Li; Xiangdong Xu; Shen Hu

doi:10.1007/978-1-0716-3323-6_13

Single-Cell Analysis of circRNA Using ddPCR

Methods Mol Biol. 2023:2689:169-177. doi: 10.1007/978-1-0716-3323-6_13.

Authors

Jiayi Peng¹, Feng Li¹, Xiangdong Xu¹, Shen Hu^{2

3

4}

Affiliations

¹ Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, USA.
² Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, USA. shenhu@ucla.edu.
³ Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. shenhu@ucla.edu.
⁴ California NanoSystems Institute, University of California, Los Angeles, CA, USA. shenhu@ucla.edu.

PMID: 37430054
DOI: 10.1007/978-1-0716-3323-6_13

Abstract

Droplet digital polymerase chain reaction (ddPCR) is a new quantitative PCR method based on water-oil emulsion droplet technology. ddPCR enables highly sensitive and accurate quantification of nucleic acid molecules, especially when their copy numbers are low. In ddPCR, a sample is fractionated into ~20,000 droplets, and every nanoliter-sized droplet undergoes PCR amplification of the target molecule. The fluorescence signals of droplets are then recorded by an automated droplet reader. Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are ubiquitously expressed in animals and plants. CircRNAs are promising as biomarkers for cancer diagnosis and prognosis and as therapeutic targets or agents to inhibit oncogenic microRNAs or proteins (Kristensen LS, Jakobsen T, Hager H, Kjems J, Nat Rev Clin Oncol 19:188-206, 2022). In this chapter, the procedures for the quantitation of a circRNA in single pancreatic cancer cells using ddPCR are described.

Keywords: Droplet digital PCR; Pancreatic cancer cells; Single-cell analysis; circRNA.

MeSH terms

Biomarkers, Tumor* / analysis
Cell Line, Tumor
Humans
Pancreatic Neoplasms / diagnosis
Pancreatic Neoplasms / pathology
Polymerase Chain Reaction* / instrumentation
Polymerase Chain Reaction* / methods
RNA, Circular* / analysis
RNA, Circular* / genetics
Single-Cell Analysis* / instrumentation
Single-Cell Analysis* / methods

Substances

RNA, Circular
Biomarkers, Tumor