The sampled structures of the brain regions profiled by RNA seq data from the human BrainSpan project


I’m looking to do analysis on the RNA-Seq Gencode v10 summarized to genes folder, from the human brain span data (found at and I was wondering if there was any detailed description for the brain regions as only the names are provided in the developmental transcriptome document in Table 2 ‘Brain regions profiled by RNA sequencing and exon microarray technologies’ (found via selecting documentation from the previous link).

In a microarray Nature article (Hawrylycz et al. 2012 - An anatomically comprehensive atlas of the adult human brain transcriptome | Nature) which uses Allen Brain Atlas data, I found a table (supplementary Table 2 – excel tab 1: SamplingOverview) that gives detailed descriptions of the brain regions of which there is some overlap and I wanted to check if this was the same for this RNA-seq data please? For example, for the brain region ‘Cerebellar Cortex’ it details the Sampled structures as ‘Cortex from the lateral hemispheres, paravermis, and vermis’.



Hi @bard-rose,

Thank you for your interest in the BrainSpan data. The brain structures all align with the Allen Reference Atlases (here or here). The abbreviations and associated names match perfectly if you download the data you linked above and open the “columns_metadata.csv” file, which includes columns about anatomical localization. These mostly, but not perfectly match the names used in Table 2.

It is also important to note that a different atlasing strategy was used for the original Allen Human Brain Atlas, which focused on the structural rather than functional areas. For example, here is the organization for occipital cortex from the Human Brain Atlas and BrainSpan, respectively:

Hopefully this addresses your question, but if not, let us know!