Polymerase Chain Reaction (PCR) and Droplet Digital PCR (ddPCR) Protocol

Katie Jing Kay Lam; Olubankole Arogundade; Claire Clelland

Nov 24, 2025

Polymerase Chain Reaction (PCR) and Droplet Digital PCR (ddPCR) Protocol

DOI

https://dx.doi.org/10.17504/protocols.io.x54v9288ml3e/v1

Katie Jing Kay Lam¹,
Olubankole Arogundade¹,
Claire Clelland²

¹Weill Institute for Neurosciences, University of California, San Francisco, USA;
²Department of Neurology, University of California, San Francisco, CA, USA

Claire D Clelland

UCSF Weill Institute for Neurosciences

DOI: https://dx.doi.org/10.17504/protocols.io.x54v9288ml3e/v1

Collection Citation: Katie Jing Kay Lam, Olubankole Arogundade, Claire Clelland 2025. Polymerase Chain Reaction (PCR) and Droplet Digital PCR (ddPCR) Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.x54v9288ml3e/v1

License: This is an open access collection distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Protocol status: Working

We use this collection and it's working

Created: March 07, 2024

Last Modified: November 24, 2025

Collection Integer ID: 97370

Keywords: droplet digital pcr, ddpcr, dna preparation, polymerase chain reaction, pcr, protocol detail, protocol this protocol, protocol, gel electrophoresi

Abstract

This protocol details the DNA preparation, polymerase chain reaction (PCR), gel electrophoresis, and droplet digital PCR (ddPCR) processes.

Attachments

pyqqbqzk7.pdf

2.9MB

Materials

 
ABC
ReagentManufacturerCatalog No.
DNA preparation
QuickExtract™ DNA Extraction SolutionBiosearch Technologies76081-768
PCR
BioMix™ RedMeridian Life SceiencesC755F25
Dimethyl sulfoxide (DMSO)Sigma Aldrich Fine  Chemicals BiosciencesD8418
Gel electrophoresis
Quick-Load® Purple 1 kb Plus DNA LadderNew England Biolabs Inc.N0550S
SYBR™ Safe DNA Gel StainInvitrogenS33102
TAE Buffer (Tris-acetate-EDTA) (50X)Thermo ScientificB49
ddPCR
ddPCR™ Copy Number Assay: RPP30, Human, Homo sapiensBio-RaddHsaCP1000485
ddPCR Supermix for Probes (No dUTP)Bio-Rad1863024
Droplet Generation Oil for ProbesBio-Rad1863005
 
 
ABC
  Equipment/Consumable 
    Manufacturer 
    Catalog No. 
  
  PCR 
  
  Thermal Cycler 
    Bio-Rad
  
     
  
  Gel electrophoresis 
  
LI-COR Odyssey M Imager LI-COR  
PowerPac™ HC Power Supply Bio-Rad  
Sub-Cell GT Horizontal Electrophoresis System Bio-Rad  
  ddPCR 
  
C1000 Touch™ Thermal Cycler with 96–Deep Well Reaction Module Bio-Rad 1851197 
ddPCR™ 96-Well Plates Bio-Rad 12001925 
DG8™ Cartridges Bio-Rad 1864008 
DG8™ Cartridge Holder Bio-Rad 1863051 
DG8™ Gaskets Bio-Rad 1863009 
PCR Plate Heat Seal, foil, pierceable Bio-Rad 1814040 
PX1 PCR Plate Sealer Bio-Rad 1814000 
QX200 Droplet Digital PCR System Bio-Rad  
 

Troubleshooting

Attachments

pyqqbqzk7.pdf

2.9MB

Files

Protocol

Name

Polymerase Chain Reaction (PCR)

Version 1

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