Dear all, I have downloaded the data of a specific gene of interest as I would like to visualize its expression overtime prenatally. In the annotation of the brain areas I see different classifications: either “top level structure name” or “structure name”. In the first one I see a classification referred to as “ventricular zone”. What does it refer to? can I include it in the cortex for my classification or does it refer to a more caudal area of the brain?
Is there a document in which I can visualize the different areas named in the downloaded data?
Ventricular zone (or “VZ”) refers to one of the layers of neocortex during prenatal development. This exists in all of the neocortical regions and therefore, on it’s own, is insufficient to tell you where the sample is coming from.
This paper (Transcriptional landscape of the prenatal human brain | Nature) describes the component of the BrainSpan atlas of the developing human brain focused on prenatal donors that has laminar dissections and could likely give you more detail. If you’d like to see some pre-built plots on this data set for your gene of interest I’d highly recommend accessing the Gene Knowledge Cards website (be patient, it is slow to load!), entering your gene of interest on the upper left and then clicking on the “Development” tab in the menu. This will give you plots showing gene expression over time in mouse, human, and rhesus macaque. These plots can also be generated using the atlasplot R library.