gene expression
Normalisation is a choice
Why library size, median-ratio, TMM and TPM answer different questions, and why the normalisation method belongs in the result.
8 October 2026 · 9 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
Pathway lists and the multiple-testing problem
How testing thousands of genes creates a multiple-testing problem, and why a pathway table built on an already chosen list is not yet a mechanism.
8 October 2026 · 10 min read
gene expression
Questions before an RNA-seq enquiry
The scientific questions to settle before an RNA-seq enquiry: organism, library chemistry, depth, replicates, integrity and the analysis you want.
8 October 2026 · 9 min read
gene expression
RNA-seq library types polyA and ribodepletion
How poly(A) selection and ribosomal depletion keep different RNA molecules, and when degraded, bacterial or non-polyadenylated samples need the broader library.
8 October 2026 · 8 min read
gene expression
RT-qPCR for relative expression
How RT-qPCR for relative expression compares transcripts, using reference genes, efficiency checks and controls that keep a fold change honest.
8 October 2026 · 8 min read
gene expression
Sample naming so a bioinformatics file matches the freezer
A naming scheme that keeps freezer tubes, metadata sheets and bioinformatics columns on the same sample, including labels that survive humidity.
8 October 2026 · 10 min read
gene expression
Single-cell RNA-seq in outline
What single-cell RNA-seq adds beyond a bulk average: droplets or wells, empty droplets, doublets, UMIs, sparse counts, and clustering as a parameter.
8 October 2026 · 7 min read
gene expression
Small RNA sequencing overview
Why small-RNA libraries fail when adapter dimers dominate, how miRNA arm bias and reference mapping differ from mRNA analysis, and how degradation can imitate a
8 October 2026 · 9 min read
gene expression
Spatial transcriptomics as a concept
How spatial transcriptomics attaches expression to a tissue coordinate, why spot and cell resolution differ, and what section quality and permeabilization
8 October 2026 · 9 min read
gene expression
Standard curves and primer efficiency
How a standard curve turns primer slope into efficiency, and how R-squared, dynamic range, no-template controls and primer dimers decide if the line is usable.
8 October 2026 · 10 min read
gene expression
Stranded libraries and transcript orientation
How stranded RNA-seq libraries keep transcript direction, and why antisense or overlapping genes are unreadable when the chemistry is unstranded.
8 October 2026 · 9 min read
gene expression
The MIQE idea in everyday language
What a qPCR report should disclose so another scientist can judge the number: sample handling, reverse transcription, primers, efficiency, reference genes and
8 October 2026 · 10 min read