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phs000406.v3.p1 : Spatiotemporal Transcriptome of the Human Brain
phs000731.v2.p1 : BrainSpan Atlas of the Developing and Adult Human Brain

Study Description

The NIH-funded BrainSpan (www.brainspan.org) and PsychENCODE (www.psychencode.org). Consortia sought to generate and analyze multi-dimensional genomics data from the developing and adult human brain in healthy and disease states. One of the main goals has been to perform large-scale and integrated analysis of the genome, transcriptome, and epigenome of the human brain to broaden our understanding of human neurodevelopment. This dataset consists of sixteen regions, including eleven neocortical areas, of human donors of both sexes and various ethnic groups. In the first stage of this project, we provide the genome-wide exon-level transcriptome data generated using the Affymetrix GeneChip Human Exon 1.0 ST Arrays, and the genome-wide genotyping data for 2.5 million markers using the Illumina Human Omni 2.5-Quad Bead Chips. In the second stage of this project, we provide whole-genome sequencing data, transcriptome data by mRNA-Seq, small RNA data by smRNA-seq, DNA cytosine methylation by Infinium HumanMethylation450 BeadChip, and epigenomic/epigenetic data by ChIP-Seq for H3K4me3, H3K27me3, H3K27ac and CTCF.

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Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. The site also contains data dictionaries, variable summaries, documents, and truncated analyses, whenever available.

Study Inclusion/Exclusion Criteria

All selected subjects are normal according to following criteria:

  1. Subjects with chromosomal or large-scale genomic abnormalities, detected by karyogram and/or Illumina Human Omni-2.5, were excluded.
  2. Prenatal and neonatal specimens were excluded if drug or alcohol abuse by the mother during pregnancy was reported or if potassium chloride, salt water, or urea were injected into the amniotic sac during surgical procedure.
  3. Only brains free of obvious malformations or lesions were collected. Disqualifying characteristics included any obvious abnormality of the neural tube, forebrain, brainstem, cranial nerves, cerebellum, or spinal cord.
  4. Samples were excluded if microscopic analysis revealed extensive neuronal loss, neuronal swelling, glioneuronal heterotopias, or dysmorphic neurons and neurites.
  5. Samples that tested positive for Hepatitis B, Hepatitis C, or HIV were excluded.
  6. Early postnatal and adult (periods 8-15) specimens were excluded if excessive drug or alcohol abuse was reported, if the individual had any known neurological or psychiatric disorders, or if any prolonged agonal conditions were reported.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
mRNA Sequencing Illumina Genome Analyzer IIX N/A N/A
smRNA Sequencing Illumina HiSeq 2000 N/A N/A
Whole Genome Sequencing Illumina Genome Analyzer IIX N/A N/A
ChIP Sequencing Illumina Genome Analyzer IIX N/A N/A
ChIP Sequencing Illumina HiSeq 2000 N/A N/A
Whole Genome Genotyping Illumina HumanOmni2.5-Quad N/A N/A
DNA Methylation Array Illumina Infinium HumanMethylation450 BeadChip N/A N/A
Exon Array Affymetrix GeneChip Human Exon 1.0 ST Array N/A N/A
Selected publications
Diseases/Traits Related to Study (MeSH terms)
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