Question

I am using the Developmental Transcriptome tool from the Allen Brain Atlas to determine at what stages of development a specific gene is expressed in the human brain.

I have read the official documentation as to how the RNA-Seq data for the Developmental Transcriptome was generated and analysed. In the documentation, it says that they used postmortem human brain specimens from a range of different developmental stages (embryonic, early prenatal, early mid-prenatal, late mid-prenatal, late prenatal, early infancy, late infancy, childhood, adulthood).

The heatmap showing the gene expression levels across the different brain samples was generated from the RNA-Seq data. I know that heatmaps show the gene expression levels in a number of samples (e.g. treatments, disease) relative to a control sample.

However, when showing the gene expression levels across the different brain samples they used, I was wondering if there is a reference brain sample that was used? E.g. they are comparing gene expression in other brain samples relative to the reference brain sample. I have read the documentation and there is nothing mentioned regarding this.

I was wondering if anyone who has used the Developmental Transcriptome tool before knows whether the gene expression levels are compared against a reference brain sample? Any insights are appreciated.

Answer 1

In the Allen Brain Atlas Developmental Transcriptome tool, gene expression levels across different brain development stages are not necessarily compared against a single reference brain sample; instead, normalization methods are used to allow direct comparison of expression levels.

Step-by-step explanation:

Regarding the question of whether gene expression levels in the Allen Brain Atlas Developmental Transcriptome tool are compared against a reference brain sample.

It is important to understand that in transcriptomic studies, a reference sample is not always necessary.

In many cases, such as the longitudinal study of brain development represented by the tool you're using, gene expression is measured across a range of brain samples representing different developmental stages without being compared to a single reference sample.

Instead, the data can be normalized to account for batch effects, sequencing depth, and other variables, which allows for the comparison of expression levels across various samples without the need for a single reference.

RNA-Seq and other high-throughput technologies provide a portrait of the transcriptome by measuring the presence and quantity of mRNA in a sample.

When generating a heatmap from such data, the colors represent the relative expression levels of genes across samples.

If the documentation does not specify using a reference brain sample, they likely used an in-built normalization method to make direct comparisons of expression levels possible.