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Status |
Public on Dec 17, 2018 |
Title |
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [RNA-Seq] |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.
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Overall design |
72 WGBS libraries were sequenced (from intact tissue (27 libraries) and NeuN+ and NeuN- flow sorted nuclei (45 libraries)) from hippocampus, nucleus accumbens, prefrontal cortex (BA9), and anterior cingulate gyrus (BA24). RNA-seq (20 libraries) and ATAC-seq (23 libraries) data from NeuN+ and NeuN- flow sorted nuclei from the nucleus accumbens and prefrontal cortex (BA9) were also obtained.
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Contributor(s) |
Rizzardi LF, Hickey P, Hansen KD, Feinberg AP |
Citation(s) |
30643296 |
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Submission date |
Mar 14, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Andrew P. Feinberg |
Organization name |
Johns Hopkins University School of Medicine
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Street address |
855 N. Wolfe St
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City |
Baltimore |
State/province |
MD |
ZIP/Postal code |
21205 |
Country |
USA |
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Platforms (1) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (20)
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This SubSeries is part of SuperSeries: |
GSE96615 |
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability |
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Relations |
BioProject |
PRJNA379175 |
SRA |
SRP101890 |