gene expression analysis Services: Quantifying Transcriptional Activity for Research & Biomarker Discovery

As an independent third-party analytical service provider, we offer comprehensive gene expression analysis for academic, pharmaceutical, biotechnology, and clinical research clients. Gene expression analysis measures the activity of specific genes or whole transcriptomes by quantifying messenger RNA (mRNA) levels, providing critical insights into cellular responses, disease mechanisms, drug effects, and biomarker identification. Our accredited laboratory follows international guidelines (MIQE, MIAME, CLSI) and employs a range of technologies – including quantitative real‑time PCR (qPCR), digital PCR (dPCR), RNA sequencing (RNA‑seq), and microarrays – to deliver accurate, reproducible, and biologically relevant data. This article outlines our gene expression analysis capabilities – including scope, key test items, and standard methods – to help researchers, clinicians, and drug developers quantify gene expression with confidence.

1. Our Testing Scope for Gene Expression Analysis

We cover a wide range of sample types, target genes, and expression scales:

By sample type: Tissues (fresh, frozen, FFPE – formalin‑fixed paraffin‑embedded); Cells (cultured, sorted, primary); Blood (whole blood, PBMCs, plasma exosomes); Biopsies (core needle, surgical); Liquid biopsies (circulating tumour cells, cell‑free RNA); Plant tissues; Microdissected samples; Single cells (after lysis).

By species: Human (all tissues, disease models); Mouse, rat, rabbit; Non‑human primates; Dog, pig, livestock; Zebrafish; Drosophila; Plants (Arabidopsis, rice, maize, etc.); Custom species (on request).

By expression scale: Targeted (few genes – up to 20 targets); Medium‑plex (21‑200 targets by microfluidic qPCR); High‑plex / whole transcriptome (RNA‑seq, microarray).

By analysis objective: Differential expression (treatment vs. control); Pathway analysis; Biomarker discovery; Pharmacodynamic response; Copy number variation (parallel DNA analysis); Splice variant quantification; Non‑coding RNA (miRNA, lncRNA, circRNA).

2. Key Test Items & Measurements We Perform

Our gene expression analysis Services are grouped by technology platform. Each approach offers specific advantages for sensitivity, dynamic range, and throughput.

2.1 Quantitative Real‑Time PCR (qPCR) – Targeted Expression

Relative quantification (ΔΔCt method) – fold‑change of target gene vs. one or more reference genes (e.g., GAPDH, ACTB, 18S, B2M).
Absolute quantification – copy number per µL RNA using a standard curve (plasmid or synthetic oligonucleotides).
Gene expression ratio (target / reference) – normalised against internal control.
High‑resolution melting (HRM) for allelic expression – optional.
Multiplex qPCR (2‑4 targets per well) – using different fluorescent dyes (FAM, VIC, NED, etc.).
Microfluidic qPCR (BioMark, Biomark HD) – 96 to 384 targets per sample with low sample consumption.
End‑point PCR (qualitative) – for simple presence/absence (not recommended for quantitation).

2.2 Digital PCR (dPCR) – Absolute Quantification Without Standard Curves

Absolute copy number (copies/µL) – direct counting of positive partitions.
Rare mutation detection – e.g., low‑abundance transcripts or minor splice variants.
Exact quantification without reference gene – useful for samples with limited inhibitors.
Comparison of two targets (e.g., tumour vs. normal allele) – ratio measured with high precision.

2.3 RNA Sequencing (RNA‑seq) – Whole Transcriptome Discovery

Bulk RNA‑seq (total RNA or mRNA‑enriched) – quantifies all expressed genes, isoforms, and non‑coding RNAs.
Differential expression analysis – using DESeq2, edgeR, or limma‑voom pipelines.
Transcript assembly and isoform quantification – identification of alternative splicing events.
Gene set enrichment analysis (GSEA) – pathway and functional annotation (GO, KEGG, Reactome).
Small RNA sequencing (miRNA, piRNA) – discovery and expression profiling.
Single‑cell RNA‑seq (scRNA‑seq) – by arrangement (10x Genomics platform).
Low‑input / degraded RNA (FFPE, microdissection) – dedicated library prep (SMART‑seq, Ribo‑zero).

2.4 Microarray – High‑Throughput Targeted Transcriptomics

Expression microarrays (Affymetrix / Illumina) – covering 20,000+ annotated genes.
Single‑channel vs. dual‑channel (Cy3 / Cy5) – direct comparison of two samples.
miRNA arrays – profiling of hundreds to thousands of mature miRNAs.
Custom arrays – for species‑specific or focused pathway panels.

2.5 RNA Quality & Sample QC

RNA integrity number (RIN) – using Agilent Bioanalyzer or TapeStation (RIN > 7 recommended for RNA‑seq).
DV200 (for FFPE samples) – percentage of RNA fragments > 200 nucleotides.
Concentration (ng/µL) – fluorometric (Qubit) or spectrophotometric (Nanodrop).
260/280 and 260/230 ratios – purity assessment (protein, phenol, salt contamination).

3. Standard Test Methods & Guidelines We Apply

All experiments are performed in accordance with best‑practice guidelines. Our laboratory follows ISO/IEC 17025 principles (where applicable) and MIQE / MIAME standards.

3.1 qPCR & dPCR Standards

MIQE (Minimum Information for Publication of Quantitative Real‑Time PCR Experiments) – guidelines for experimental design, amplification efficiency, and data analysis.
RDMI guideline for dPCR (Minimum Information for Digital PCR).
CLSI MM13 (Quantitative molecular methods for infectious diseases).
ISO 20395 (Requirements for validation of PCR‑based methods).

3.2 RNA‑seq & Microarray Standards

MIAME (Minimum Information About a Microarray Experiment) – for microarray studies.
ENCODE guidelines (for RNA‑seq library preparation and analysis).
FAIR data principles (Findable, Accessible, Interoperable, Reusable).
CAP / CLIA (for clinical gene expression profiling – by arrangement).

3.3 Sample Processing & QC Standards

ISO 20186 (Molecular in vitro diagnostics – pre‑examination processes for RNA).
CLSI MM19 (Establishing molecular testing in clinical laboratories).

4. Why Choose Our Third‑Party gene expression analysis Services?

As an independent laboratory specialising in molecular biology, we provide accurate, reproducible, and publication‑ready data. Our advantages include:

ISO/IEC 17025 accreditation (for select methods) – with strict adherence to standard operating procedures and quality control.
Multiple platforms – qPCR, dPCR, RNA‑seq (Illumina NovaSeq), microarray (Thermo Clariom) – we select the right tool for your research question.
Experienced bioinformatics support – raw data processing, normalisation, differential expression, pathway analysis, and custom figures.
Low sample input – qPCR from as little as 1 pg total RNA; RNA‑seq from 10 pg (with amplification).
High throughput – up to 384 samples per qPCR run; 48 samples per RNA‑seq lane.
Fast turnaround – qPCR: 5‑7 business days; RNA‑seq: 3‑4 weeks (including bioinformatics).
Detailed reporting – for qPCR: Ct values, melt curves, amplification plots, normalised fold‑change, statistics; for RNA‑seq: read counts, TPM, FPKM, differential tables, PCA plots, heatmaps, and GSEA results.
Confidentiality – full protection of your research objectives and proprietary gene targets.
Consultative support – our scientists assist with experimental design, reference gene selection, power analysis, and data interpretation.

Whether you need to validate a few candidate biomarkers by qPCR, profile the whole transcriptome of treated vs. control cells, or detect rare transcripts using dPCR, our gene expression analysis experts are ready to deliver precise, actionable results that accelerate your research and development.

Get Started with Your Gene Expression Analysis Project

Contact our team with your species, sample type (number and type), target genes or pathways, desired technology (qPCR, dPCR, RNA‑seq, microarray), and analysis requirements (relative quantification, absolute, differential expression). We will provide a detailed quotation, sample submission guidelines (RNA extraction if not performed in‑house), and a testing schedule. Let us help you decode transcriptional activity with reliability and speed.

This article provides an overview of our gene expression analysis capabilities. For specific assay designs, sample numbers, and pricing, please request a tailored service proposal.