The fundamental toolkit of proteins and other molecules are shared by every cell in an organism, but are used in different combinations at different times. One way these combinations are selected is via regulatory DNA called enhancers which interact with a class of proteins called transcription factors. These in turn affect which cellular tools are manufactured for further use in the cell. Since regulatory DNA sequence changes very little from cell to cell, every cell has the full set of instructions and yet is able to follow only the part that is relevant to its place in the organism.
The process of development from a fertilised egg to an adult is an amazing instance of this, and is the context in which I have developed models at the single-cell level in Drosophila.
In addition, I have been developing methods to analyse single-cell RNA-seq data in Ciona, a marine chordate, and have been collaborating with the Luscombe Unit to build the capacity to answer specific questions on regulation in a related organism, Oikopleura dioica.
Crocker, J., Ilsley, G. R. & Stern, D. L. Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nat Genet 48, 292–298 (2016).