I am a Master’s student working on an Adverse Outcome Pathway (AOP) framework. I am particularly interested in understanding the expression profile of the SCN2A gene (Voltage gated sodium channel) in oligodendrocytes (OL) and oligodendrocyte progenitor cells (OPC) during human development over time. Could you please guide me on how to locate this cell-type-specific information for this gene in the Developmental Transcriptome dataset?
The short answer is that what you want to do is not possible using any single Allen Brain Atlas, but that you might be able to learn something by combining a few.
The Developmental Transcriptome data set could tell you how SCN2A gene expression changes across ALL cell types from early prenatal human to middle-age adult. As this is bulk data, you cannot directly separate gene expression in different cell types.
The Prenatal LMD Microarray data set will give you gene expression levels are more precise anatomic dissections (e.g., different cortical layers) for a few donors from 15-21pcw, which may be a shorter range of developmental ranges that you need.
Finally, you could use the Transcriptomics Explorer or ABC Atlas to see which cell types SCN2A is expressed in in adults. If this SCN2A is primarily found in OL/OPC types, then the bulk data might be sufficient, but if it is more widely expressed, or if it has higher expression in neurons, then the bulk data may not be useful at all.
There are some single cell RNA-seq data sets in developing human brain available from other groups that may also be useful, including this one from the Kriegstein lab.