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Allen Brain Atlas API

The BrainSpan Atlas of the Developing Human Brain is a foundational resource for studying transcriptional mechanisms involved in human brain development. Data includes:

  • 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

From the API, you can:

Download expression values
Query the correlative and differential search services

Experimental Overview and Metadata

Developmental Transcriptome

The Developmental Transcriptome Study is a broad developmental survey of gene expression in specific brain regions using RNA sequencing and exon microarray techniques. The survey profiles up to sixteen targeted cortical and subcortical structures across the full course of human brain development, spanning pre- and postnatal-development in both males and females.

Each sampling site is associated to a Structure. Structures are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical positions in the brain.

See the structure ontology page for more information.

Typically, for each sample four typs of expression values are available:

  • RNA-Seq RPKM values summarized to a gene level
  • RNA-Seq RPKM values summarized to an exon level
  • Normalized exon microarray expression values summarized to a gene level
  • Normalized exon microarray expression values summarized to a probeset level

Normalized expression values can be downloaded in several ways:

  • From the web application Download page.
  • From the "Download this data" link below the heatmap in the web application.
  • From the connected data service in the API

All experimental data from this study is associated with the "Developing Human Transcriptome" Product. All gene, exon, probeset, donor and sampling site information can be accessed through the API using RMA queries.

Examples:

Prenatal LMD Microarray

The Prenatal LMD Microarray Study is a genome-wide microarray data profiling gene expression in finely dissected regions spanning the entire prenatal human brain and isolated using laser capture microdissection.

RNA isolated from each sample area was hybridized to a custom Agilent 8x60k microarray chip to measure gene expression over the transcriptome. All least two different probes were available for 93% of genes. Probes were located on different exons as much as possible when multiple probes were available for a gene. For 60 genes, a set of tiling probes were probes was designed. This study uses the same chip design as the Human Brain Microarray Survey.

Each sampling site is associated to a Structure by expert anatomist using cytoarchitectural information from multiple histological stains. Structures are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical positions in the brain.

See the structure ontology page for more information.

Normalized microarray expression values can be downloaded in several ways:

  • From the web application Download page. Each zip file contains the normalized values for all probes and all samples for one donor )
  • From the "Download this data" link below the heatmap in the web application.
  • From the connected data service in the API

All experimental data from this study is associated with the "Developing Human Prenatal LMD Microarray" Product. All probe and sampling site information can be accessed through the API using RMA queries.

Examples:

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