gene expression
A glossary of expression terms
Plain definitions of Cq, TPM, counts, FDR, UMIs and the other expression words that cause arguments when they are used loosely.
8 October 2026 · 11 min read
Topic cluster
Gene expression
From RNA quality to RT-qPCR and RNA-seq, including controls, normalisers and the limits of a fold-change claim.
All topicsBuffers and laboratory water26Cell culture26Chromatography26Cold chain and sample storage26Cytometry and microscopy26DNA sequencing26Gels and blotting26Gene expression26Genome editing26Immunoassays26Laboratory labware26Laboratory safety26Liquid handling26Microbiology26Molecular cloning26Nucleic acid purification26PCR and amplification26Protein biochemistry26Proteomics26Research sourcing and study design26
sequencingrna seqstudy designrt qpcrreportinglibrary prepmetadatano rt controltissuebatch effectsfdrgene expressionnormalisationprimer dimerprimersqpcrreference genesreplicates
26 articles
gene expression
A heatmap is a picture not a conclusion
How clustering, colour scale and row scaling change a gene-expression heatmap, and why the differential table and the contrast remain the result.
8 October 2026 · 8 min read
gene expression
Batch effects in an expression study
What a batch effect is in an expression study, how library date, operator, sequencer or kit lot can dominate a PCA, and what a correction model can adjust.
8 October 2026 · 8 min read
gene expression
Biological versus technical replicates
How to tell a biological replicate from a technical one, and which unit of inference actually supports a treatment claim in an expression study.
8 October 2026 · 8 min read
gene expression
Choosing reference genes instead of hoping
How to choose reference genes for this experiment by testing stability, instead of trusting a housekeeping name such as GAPDH or ACTB from another study.
8 October 2026 · 9 min read
gene expression
Comparing RT-qPCR and RNA-seq on the same question
Why RT-qPCR and RNA-seq can disagree on one gene, and when that disagreement means they measured different molecules rather than a failed assay.
8 October 2026 · 8 min read
gene expression
Delta-delta Cq and what it assumes
What delta-delta Cq assumes about efficiency, the calibrator and reference genes, and why the fold change is a relative comparison under those conditions.
8 October 2026 · 8 min read
Pillar · gene expression
From cells to a gene expression result
How a laboratory goes from cells to a gene expression result, and how RNA quality decides between a focused RT-qPCR assay and RNA-seq.
8 October 2026 · 7 min read
gene expression
How many replicates a simple design needs to discuss
What to write when a simple expression design asks for replicates: the biological unit, why one sample cannot carry a treatment claim, and why pilots exist.
8 October 2026 · 9 min read
gene expression
Inhibition and weird Cq values
How late, early or impossible Cq values point to inhibition, primer-dimer or a failed control, and which check separates those causes.
8 October 2026 · 9 min read
gene expression
Intron-spanning primers and genomic DNA
How intron-spanning primers make genomic DNA a different product from cDNA, and when a no-RT control is the only honest check.
8 October 2026 · 9 min read
gene expression
Low-input RNA and amplification bias
When a low-input RNA method is the right class, and how extra amplification and missing UMIs distort the proportions you meant to measure.
8 October 2026 · 9 min read