Single-cell analysis

Compared to traditional methods of analyzing cell populations in bulk, single-cell analysis can obtain data at the single-cell level, helping researchers better understand cellular heterogeneity, biological functions, processes and disease mechanisms. Commonly used methods for single-cell analysis, including PCR, qPCR or next-generation sequencing (NGS) sometimes lack the sensitivity required to detect the target of interest.

Digital PCR is an emerging option for single-cell analysis, due to cost-efficient, intuitive and accurate dPCR platforms that offer high throughput, high sensitivity of detection and precision.

Benefits of using nanoplate dPCR for single-cell analysis

Highly accurate with physical partitioning that is more stable than droplets
Probe-based detection allows for multiplexing of up to 12 targets in a single dPCR reaction with minimal optimization
Precise results enable analysis of low abundance targets and multi-copy targets at a single-cell level

Multiplex digital PCR for analysis of gene expression at a single-cell level

Single-cell gene expression analysis allows us to capture individual cell heterogeneity rather than the average output of a cell population. Transcriptome analysis using common PCR- and NGS-based techniques often lacks the sensitivity required to detect low-abundance single-cell targets. Digital PCR is the go-to method for absolute quantification of RNA targets, enabling subtle changes in the expression of target genes to be studied down to a single-cell level. In this application note, discover a workflow that combines high-accuracy single-cell isolation with nanoplate-based dPCR for high-throughput analysis of gene expression in cultured cells.

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Related publications

Dirkx L et al. Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites. PLoS Pathog. 2024;20(4).

Luo Y, Viswanathan R, Hande MP, Loh AHP, Cheow LF. Massively parallel single-molecule telomere length measurement with digital real-time PCR. Sci Adv. 2020;6(34).

Further resources

Thorn J et al. A workflow combining high-accuracy cell sorting with digital PCR for analysis of miRNAs in defined cell pools and single cells. QIAGEN and cellenONE, 2024.

Albers J et al. A workflow combining high-accuracy cell sorting with multiplex digital PCR for mitochondrial and genomic target copy number analysis. QIAGEN and cellenONE, 2024.