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Single cell analysis by qPCR for targeted gene expression profiling

AnyGenes® provides qPCR-based solutions for single cell analysis, combining direct lysis, specific preamplification and SignArrays® qPCR arrays to support targeted gene expression profiling from very limited biological material.

Designed for researchers working with rare cells, low-input samples or selected cell populations, this workflow helps analyze genes, biomarkers and signaling pathways using a streamlined qPCR approach.

Single cell qPCR Direct lysis Preamplification SignArrays®
Single cell analysis by qPCR using direct lysis preamplification and SignArrays gene expression profiling

Single cell analysis at a glance

AnyGenes® single cell qPCR solutions are designed for projects requiring targeted gene expression analysis from individual cells, rare cell populations or low-input biological samples.

Low-input qPCR workflow

Supports gene expression analysis from very limited biological material, including rare or sorted cells.

Direct lysis with DiLysis™

Helps simplify sample preparation while reducing RNA loss associated with conventional extraction steps.

Specific preamplification with SpeAmp®

Supports targeted amplification of selected cDNA targets before qPCR analysis.

SignArrays® pathway profiling

Enables targeted analysis of selected signaling pathways and biomarker panels by qPCR.

Gene expression analysis

Designed for targeted quantification of selected genes, transcripts or pathway signatures.

Compatible qPCR ecosystem

Can be combined with AnyGenes® validated primers, Master Mixes and data analysis tools.

A qPCR workflow for single cell and low-input samples

Single cell analysis by qPCR requires careful control of each experimental step, from cell collection and lysis to reverse transcription, preamplification, qPCR and data interpretation.

AnyGenes® combines DiLysis™, SpeAmp® and SignArrays® to support a targeted workflow for gene expression profiling when starting material is limited.

1. Direct lysis

DiLysis™ helps prepare cell lysates while limiting sample handling and potential RNA loss.

2. Reverse transcription and preamplification

SpeAmp® supports specific preamplification of selected targets before qPCR analysis.

3. qPCR pathway profiling

SignArrays® and validated qPCR assays can be used to profile selected genes and signaling pathways.

For low-input samples, assay design, sample handling, reverse transcription efficiency, preamplification strategy and normalization remain critical for reliable interpretation.

Select your single cell qPCR workflow components

Combine direct lysis, specific preamplification and SignArrays® qPCR arrays to support targeted gene expression analysis from rare cells, low-input RNA samples and limited biological material.

Preamplification kits — SpeAmp® reagents

SpeAmp preamplification reagents for single cell qPCR and low-input gene expression analysis

SpeAmp® reagents support efficient and specific preamplification for rare samples, low-input RNA workflows and targeted gene expression analysis before qPCR.

  • specific preamplification of selected cDNA targets;
  • analysis of up to 4 signaling pathways from 5–50 ng of RNA;
  • support for weakly expressed or low-abundance genes;
  • compatible with SignArrays® qPCR arrays;
  • suitable for rare samples and low-input workflows.

Direct lysis reagents — DiLysis™ range

DiLysis direct lysis reagents for single cell qPCR and rare cell samples

DiLysis™ reagents support direct lysis workflows for single cell analysis and low-input qPCR, helping reduce sample handling and potential RNA loss before downstream gene expression analysis.

  • direct lysis workflow for limited biological material;
  • support for signaling pathway analysis from approximately 10–100 cells;
  • reduced sample handling compared with conventional RNA extraction;
  • designed to help preserve RNA integrity in low-input workflows;
  • compatible with reverse transcription, SpeAmp® preamplification and qPCR analysis.
Input ranges and workflow performance depend on sample quality, target abundance, reverse transcription efficiency, preamplification strategy, assay design and the selected SignArrays® panel.

Applications of single cell analysis by qPCR

AnyGenes® qPCR solutions can support targeted analysis of rare cells, low-input samples and selected biological pathways.

Rare cell populations

Analyze gene expression in limited cell populations obtained by sorting, isolation or enrichment.

Cellular heterogeneity

Explore selected gene expression differences between individual cells or defined cell groups.

Immune cell profiling

Study selected immune markers, cytokines or pathway genes in low-input immune cell samples.

Cancer research

Support targeted analysis of tumor cells, rare cell populations or selected biomarker candidates.

Stem cell and differentiation studies

Analyze selected genes involved in cell identity, differentiation or developmental pathways.

RNA-seq validation

Validate selected transcriptomic findings using targeted qPCR assays when starting material is limited.

Compatible qPCR tools for single cell profiling

Single cell analysis by qPCR can be strengthened by combining direct lysis, preamplification, validated qPCR primers, Master Mixes and SignArrays® pathway panels within a coherent workflow.

Validated qPCR primers

Use experimentally validated primer sets to analyze selected gene targets by real-time PCR.

qPCR Master Mixes

Combine single cell workflows with compatible SYBR® Green or probe-based qPCR reagents.

SignArrays® qPCR panels

Profile selected signaling pathways or build personalized panels using your genes of interest.

Why choose AnyGenes® for single cell analysis?

AnyGenes® combines expertise in qPCR, gene expression analysis, preamplification and pathway-focused profiling to support targeted single cell and low-input workflows.

qPCR workflow expertise

Support for experimental strategy, assay selection and targeted gene expression analysis.

Low-input sample support

DiLysis™ and SpeAmp® are designed for workflows involving limited biological material.

Pathway-focused profiling

SignArrays® panels can help analyze selected signaling pathways and biomarker signatures.

Compatible product ecosystem

Combine lysis, preamplification, validated primers, qPCR reagents and data analysis tools.

Custom panel support

Personalized SignArrays® can be designed according to your selected genes and research objectives.

Scientific support

AnyGenes® can help adapt the workflow to your sample type, input level and target genes.

Scientific publications referencing AnyGenes® technologies

AnyGenes® reagents and related technologies have been referenced in peer-reviewed scientific publications, including journals such as Nature, Circulation and PLOS ONE.

These publications illustrate the use of AnyGenes® technologies in molecular biology, gene expression analysis and biomarker-focused research workflows.

Need support for your single cell qPCR workflow?

AnyGenes® can help you select the appropriate direct lysis, preamplification, qPCR assay and SignArrays® workflow according to your sample type, target genes and research objective.

Whether your project involves rare cells, low-input samples, pathway profiling, biomarker validation or RNA-seq follow-up, our team can help define a targeted qPCR strategy.

Frequently asked questions about single cell analysis

What is single cell analysis by qPCR?

Single cell analysis by qPCR is a targeted approach used to quantify selected gene expression markers from individual cells or very small cell populations using real-time PCR.

Why is direct lysis useful for single cell qPCR?

Direct lysis can reduce sample handling and help limit RNA loss, which is important when working with individual cells, rare cell populations or low-input samples.

Why is preamplification important in low-input qPCR?

Preamplification increases the amount of selected cDNA targets before qPCR, which can help analyze weakly expressed genes or limited input material.

Can single cell qPCR be used for signaling pathway analysis?

Yes. Single cell qPCR workflows can be combined with selected SignArrays® panels to profile genes involved in signaling pathways or biomarker-focused research.

Are AnyGenes® single cell solutions compatible with validated qPCR primers?

Yes. AnyGenes® single cell workflows can be combined with validated qPCR primers, qPCR Master Mixes and SignArrays® panels for targeted gene expression analysis.

Can AnyGenes® help design a custom single cell qPCR workflow?

Yes. AnyGenes® can help select direct lysis, preamplification, qPCR assays and SignArrays® panels according to your sample type, input level and selected genes.

Need more technical answers?

Visit the AnyGenes® Help & FAQ section for detailed information about our products, services, ordering process and technical support.

Visit Help & FAQ