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BrainSpan Atlas of the Developing Human Brain

This is the online help for the BrainSpan atlas of the developing human brain web application.


BrainSpan, an atlas of the developing human brain is designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. Upon completion in 2012, the atlas will contain a variety of data modalities and cover several developmental stages. The data will include:

Gene expression data - transcriptome profiling measured by RNA Sequencing 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.

Transcriptome Profiling Data

For each gene, exon level RNA sequence (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 287 structures obtained by Laser Capture Micro dissection (LCM) at the developmental stage of 21 post-conception weeks.

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.

Reference Atlas

A full color, high-resolution, digital atlas accompanied by a hierarchically organized taxonomy of developing human brain structures is available for the developmental stage of 21 post-conception weeks. It consists of 81 annotated coronal sections spanning the rostro-caudal extent of the brain at 500-1200 micron intervals.

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