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BrainSpan: Atlas of the Developing Human Brain

An atlas of the developing human brain designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. The atlas consists of a variety of data modalities and data mining tools. Developmental Transcriptome: RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across the full course of human brain development. Prenatal LMD Microarray: High-resolution neuroanatomical transcriptional profiles of ~300 distinct structures spanning the entire brain for four midgestional prenatal specimens. In Situ Hybridization (ISH): High-resolution in situ hybridization image data covering selected genes and brain regions in developing and adult human brain. Reference Atlas: Full color, high-resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data. The NIF Data Federation currently indexes the 4 Developmental Transcriptome BrainSpan datasets: RNA-Seq exons, RNA-Seq exons summarized to genes, Exon microarray summarized to probe sets, and Exon microarray summarized to genes. The BrainSpan atlas was developed by a consortium consisting of the Allen Institute for Brain Science; Yale University (Nenad Sestan, Mark B. Gerstein); the Zilkha Neurogenetic Institute of the Keck School of Medicine of the University of Southern California (James A. Knowles, Pat Levitt); the Athinoula A. Martinos Center at Massachusetts General Hospital/Harvard Medical School and MIT HST/CSAIL (Bruce Fischl); the University of California, Los Angeles (Daniel H. Geschwind); and the University of Texas Southwestern Medical Center (Hao Huang), with strong collaborative support from the Genes, Cognition and Psychosis Program, which is part of the Intramural Research Program of NIMH, NIH (Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger).

URL: http://brainspan.org/

Resource ID: nif-0000-10626     Resource Type: Resource     Version: Latest Version


anatomic, gene expression, molecular neuroanatomy, in situ hybridization, human, medial prefrontal cortex, primary visual cortex, hippocampus, amygdala, ventral striatum, postnatal, development, brain development, transcription, brain, rna sequencing, exon microarray, developmental stage, male, female, mrna transcript, developing human, adult human, fetal brain, fetus, histology, transcriptome, magnetic resonance imaging, diffusion tensor imaging, annotation, neuroanatomy, prenatal, development, fiber tract, microarray, mri, dti, methylation, microrna, mrf

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Resource PubMed IDs

PMID: 22539971, PMID: 23193282, PMID: 23193282, PMID: 23717525, PMID: 23917947, PMID: 24285197, PMID: 24399358, PMID: 24564186, PMID: 24695229, PMID: 24695229, PMID: 24884593, PMID: 25002837, PMID: 25057125, PMID: 25191221, PMID: 25403753, PMID: 25403753, PMID: 25414627

Related To

Resource:NIH Blueprint NHP Atlas, Resource:Allen Developing Mouse Brain Atlas,



Parent Organization

Resource Status

Last checked up;


BrainSpan - Atlas of the Developing Human Brain, NIMH Transcriptional Atlas of Human Brain Development

Additional Resource Types

reference atlas, expression atlas

Related Disease

Neurodevelopmental disorder, Neuropsychiatric disease, Schizophrenia, Epilepsy, Parkinson's disease, Alzheimer's disease, Normal, Neurological disease, Autism



Original Submitter


Version Status


Submitted On

12:00am July 22, 2011

Originated From


Changes from Previous Version

First Version

Version 1

Created 4 years ago by Anonymous