Query on SCN2A Expression in OL and OPC in the Developmental Human Transcriptome Dataset

1

Hello,

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?

Thank you for your assistance!

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Hi @Li_25,

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.

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Thank you for the detailed response! It’s really helpful to have some direction on where to start with the human data.

Do you happen to know of any similar datasets, perhaps focused on rodents, that would provide comparable information on gene expression across different developmental stages or cell types? Specifically, I’m looking for datasets that could offer insights into the expression of the SCN2A gene in glial cells and neurons seperately during development in rodents.

Any recommendations would be greatly appreciated!

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The short answer is I don’t know, but hopefully other folks can chime in.

The slightly longer answer is that the Allen Institute has a Developing Mouse Brain Atlas (https://developingmouse.brain-map.org), but unfortunately, this does not include the gene SCN2A. We also have recently added an aging mouse study to the ABC Atlas (Allen Brain Cell Atlas - brain-map.org; scroll about halfway down), but this doesn’t cover prenatal or early postnatal stages. My suggestion would be do to a Google search. I’ll also follow-up with scientists at the Allen Institute who, if they have any other suggestions, will post it in this thread.