Transcriptomics: From Gene Expression to Single-Cell & Spatial RNA-Seq

Transcriptomics = the study of the complete collection of all RNA transcripts in an organism (the transcriptome). The central goal is to quantify gene expression levels.

The central dogma & RNA's fates: information flows DNA → (transcription) → RNA → (translation) → Protein. DNA can also self-replicate, and reverse transcription runs the arrow backward (RNA → DNA). Crucially, not all RNA is translated — RNA can instead act as a scaffold, a ribozyme, or regulatory non-coding RNA (ncRNA).

Gene content of the human genome:

• ~20,000 protein-coding genes
• ~25,000 pure RNA-coding (non-coding) genes

So thousands of human genes produce ncRNA as their ultimate product (gene → RNA, with no protein).

Genes are expressed with different efficiencies. How much product a gene yields depends on three things:

• Efficiency of transcription
• Stability of the mRNA
• Efficiency of translation

A highly expressed gene produces many RNA copies (and much protein); a weakly expressed gene produces few. Transcriptomics measures these differences across genes, tissues, and conditions.