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BrainSpan specifications


Unique identifier OMICS_17879
Name BrainSpan
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Ed Lein

Publication for BrainSpan

BrainSpan citations


Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia Specific Potential Biomarkers

PMCID: 5932158
PMID: 29755398
DOI: 10.3389/fneur.2018.00266

[…] To assess the microglia dynamics throughout the age (pre- and postnatal) of a human being, we utilized the human developmental transcriptome data (BrainSpan) deposited in the Allen Brain database (, ). Replicate samples for each developmental stage (prenatal or postnatal) were considered for analysis. The age groups ranged from prenatal stages, […]


Rostrocaudal Areal Patterning of Human PSC Derived Cortical Neurons by FGF8 Signaling

PMCID: 5917473
PMID: 29707616
DOI: 10.1523/ENEURO.0368-17.2018

[…] man fetal brains () were downloaded from ArrayExpress (E-MEXP-2700), normalized using fRMA (). The RNA-seq data (FPM values) of 12 and 13 pcw micro-dissected human fetal brains were obtained from the BrainSpan database () and quantile normalized. We compared our microarray dataset with these datasets with ExAtlas software (). First, data were preprocessed by log-transformation and removing outlier […]


Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

BMC Genomics
PMCID: 5905132
PMID: 29665773
DOI: 10.1186/s12864-018-4649-2

[…] tion explains the majority of brain transcriptome changes during prenatal and new-born postnatal development []. Therefore, we took the advantage of fetal and early postnatal brain RNA-seq dataset in BrainSpan and another age series RNA-seq data [], to compare the brain transcriptome before and after postnatal day 100. Remarkably, 28 out of the 33 discriminating modules showed significant concorda […]


Gene expression links functional networks across cortex and striatum

Nat Commun
PMCID: 5897339
PMID: 29651138
DOI: 10.1038/s41467-018-03811-x

[…] For the cortical Brainspan data, 18,597 unique probes possessed matching Entrez IDs to the AHBA data and non-zero levels of expression across all samples. Duplicate probes were collapsed for each donor by selecting th […]


High resolution temporal and regional mapping of MAPT expression and splicing in human brain development

PLoS One
PMCID: 5892924
PMID: 29634760
DOI: 10.1371/journal.pone.0195771
call_split See protocol

[…] rs. The microarray data are available in the NIH Gene Expression Omnibus (GEO) as GSE25219 (Yale) [], GSE30272 (Lieber) [, ] and GSE60863 (UK/NABE) [], while the RNA-sequencing data is available from BrainSpan []. The UK/NABE data do not include any cases below the age of sixteen years. Quality control and normalization was performed on each dataset by the original authors using different mathemat […]


Mob2 Insufficiency Disrupts Neuronal Migration in the Developing Cortex

PMCID: 5857600
PMID: 29593499
DOI: 10.3389/fncel.2018.00057

[…] Allen Mouse Brain Atlas database: Human Brain Science Atlas: Aggregation Consortium (ExAC), Cambridge, MA, USA http://exac.broadinstitute.orgPubMed, Mendelian Inheritance in Man (OMIM), http://www.o […]

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BrainSpan institution(s)
Allen Institute for Brain Science, Seattle, WA, USA; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Computer Science and AI Lab, MIT, Cambridge, MA, USA; Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, and Department of Computer Science, Yale University, New Haven, CT, USA; Program in Neurogenetics, Department of Neurology and Semel Institute David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA; Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Advanced Imaging Research Center, UT Southwestern Medical Center, TX, USA; Zilkha Neurogenetic Institute, and Department of Psychiatry, University of Southern California, Los Angeles, CA, USA; Department of Pediatrics, Children’s Hospital, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
BrainSpan funding source(s)
This work was supported by Award Number RC2MH089921 from the National Institute of Mental Health.

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