Part II: Transcriptomics
Measuring Gene Expression
Transcriptomics captures a snapshot of all RNA molecules in a cell or tissue at a given moment, revealing which genes are active and at what levels. From microarray technology to RNA-seq and cutting-edge single-cell approaches, transcriptomic methods have revolutionized our understanding of gene regulation, cell identity, and disease mechanisms. This part covers the technologies, computational methods, and biological insights of transcriptome analysis.
~5%
Genome Transcribed
10⁴–10⁵
Genes per Experiment
Single Cell
Resolution Frontier
Topics in This Part
5. Gene Expression & the Transcriptome
Transcription regulation, mRNA processing, transcriptome complexity, and expression quantification fundamentals
6. Microarray Technology
Probe design, hybridization chemistry, normalization methods, differential expression analysis, and clinical applications
7. RNA-Seq: Principles & Analysis
Library preparation, read alignment, transcript quantification (TPM, FPKM), DESeq2/edgeR, and pathway enrichment
8. Single-Cell & Spatial Transcriptomics
Droplet-based scRNA-seq, cell clustering, trajectory inference, spatial transcriptomics (MERFISH, Visium), and cell atlases