The transcriptome of an organism, for example an algal cell, is the set of messenger RNA (mRNA) molecules or "transcripts," produced in one cell or a population of cells. The transcriptome can cover the transcripts of an entire organism, or a specific subset of transcripts present in only one particular cell type (this is relevant for multicellular algae).

Transcription of DNA into mRNA  is one of the first steps in the regulation of cellular processes by the genes of that cell. The transcriptome can vary with growth conditions or with developmental stage of the cell. Information about the transcript levels is needed for understanding how genes control the cellular processes in response to changes inside or outside the cell. It may also reveal how genes interact to each other in so-called gene regulatory networks.

Transcriptomics, also called genome-wide expression profiling, is one of the tools which is used to understand how a cell controls biological processes: for example metabolic pathways leading to economically valuable compounds, or cellular processes which control growth rate of cell division. Transcriptomics help to resolve questions such as: what are the functional roles of different genes and in what cellular processes do they participate? How are genes regulated and how do genes and gene products interact? How do gene expression levels differ in various cell types and states and how is gene expression changed by various treatments or environmental stimuli?

Common technologies for genome-wide or high-throughput analysis of gene expression are cDNA microarrays, oligo-microarrays, cDNA-AFLP, SAGE and cDNA sequencing. Microarrays are particularly valuable when the genome of the organism of interest is already known and many thousands of individual cDNA’s or oligo’s are available. For a few organisms prefabricated expression microarrays are available. cDNA sequencing is particularly suitable when the genome sequence is unknown and when cDNA are hardly available.

Relative expression of a small subset of genes spotted on a cDNA microarray
(White spots represent highly expressed genes, black spots represent lowly or not expressed genes.)