How to: BrainSpan Atlas of the Developing Human Brain

How To Brainspan Atlas of the Developing Human Brain
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This is the online help for the BrainSpan Atlas of the Developing Human Brain web application.

The BrainSpan Atlas of the Developing Human Brain is designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. The atlas contains a variety of data modalities and covers several developmental stages. The data includes:

Gene expression data - transcriptome profiling measured by RNA sequencing (RNA-Seq) and exon microarray, microarray expression for finely sampled structures and in situ hybridization (ISH)
Anatomic data - reference atlases, MRI, histology

The currently available dataset is described below. For complete details please see the White Papers on our Documentation page.

Key Features

Transcriptome Profiling Data
RNA-Seq and exon array expression data are available for 13 stages of development over 16 structures.

Microarray Data for Finely Sampled Prenatal Structures
Microarray data are available for ~300 structures obtained by laser microdissection (LMD) at midgestational developmental stages (15-21 pcw) of four male and female donors.

In Situ Hybridization (ISH) Data
Gene expression data is available as colorimetric in situ hybridization (ISH) for specific brain regions. Images are grouped into image series that comprise an experiment. Experiments consist of slides from the same specimen that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular gene.

References Atlases
Full color, high-resolution digital atlases accompanied by a hierarchically organized taxonomy of developing human brain structures are available. Fully annotated coronal sections spanning the rostro-caudal extent of the brain at 500-3400 micron are available for 15 pcw, 21 pcw and 34 years. A brainstem atlas at 21 pcw is available at 250-500 micron intervals.

Developing Human Reference Atlases
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Dear all, I have downloaded the data of a specific gene of interest as I would like to visualize its expression overtime prenatally. In the annotation of the brain areas I see different classifications: either “top level structure name” or “structure name”. In the first one I see a classification referred to as “ventricular zone”. What does it refer to? can I include it in the cortex for my classification or does it refer to a more caudal area of the brain?

Is there a document in which I can visualize the different areas named in the downloaded data?

Thank you!

Anna