What Is a Transcriptome?

Fabian Theis calls a transcriptome the messenger RNAs each cell reads off a genome that the Human Genome Project mapped for the body and that stays pretty much the same everywhere. Different cell types exist because each cell reads different material off that genome. The messenger RNAs encode downstream proteins and are expressed differently from cell to cell. A human has something like 20,000 different types, and splicing produces many more.

Each cell is a 20,000-dimensional vector: zeros where a messenger RNA is absent, and counts of how many of the messenger RNAs are present. The messenger RNAs are called transcripts, and together they are the transcriptome. The 20,000-dimensional space is very often encoded in a nicer latent space, a subspace where the cell cloud lives. Each point is one cell. When points cluster, they are cell types. When points form a sausage, they are trajectories, like a fertilized egg cell making all the cell types in the body.