Documentation: BrainSpan Atlas of the Developing Human Brain

Documentation for BrainSpan

Document Description
Developmental Transcriptome Overview of methods for transcriptome profiling
Prenatal LMD Microarray Overview of methods for prenatal laser microdissection microarray analysis
In Situ Hybridization Overview of methods for ISH studies
Gene List Complete list of ISH genes and corresponding anatomical structure(s) with ISH data available
Reference Atlases Overview of methods for the reference atlases
Developing Human Brain Imaging Overview of methods for structural and connectional imaging data
Ontology and Nomenclature Rationale and sources for the ontology and anatomical nomenclature
Donor and Sample Metadata Metadata for donors and samples
Acknowledgements The many people and organizations that have contributed to this project

Hi, I’m looking for a pdf or txt file that documents the Donor and Sample metadata (Brain code’, ‘Allen Institute ID’, ‘Age’, ‘Region/Area’, ‘Hemisphere’, ‘RIN’, ‘Dissection score’, ‘External ID’, ‘Internal ID’, ‘Age’, ‘PMI’, ‘pH’, ‘Gender’, ‘Ethnicity’.). I’ve checked the downloads page (, but am unable to find and it is not in any of the links above.

Any help is much appreciated!


Reference_Atlas.pdf (1.3 MB)

Hi Leana,
I have attached a PDF of the white paper.
Thanks for your interest,

Hi everyone,

I was wondering why there is information about only 4 samples. when in fact we have a lot more in the RNAseq data.

@victortoledo: The donor information in the sheet above refers to the donors in the Reference Atlas, three of which were also used in the Prenatal LMD Microarray Dataset. To find donor information (IDs, age, and sex) for the RNAseq data donors, download the relevant RNA-seq data set here, and then look at the “columns_metadata.csv” file. This will give you information for each sample (donor info + brain region), so there are repeats per donor, but you should have what you need.

@leana.king: The download listed above has some of the information you are looking for, if you wanted it for the RNA-seq donors. This post has some additional information that might help.