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Series GSE96613 Query DataSets for GSE96613
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
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.
 
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.
 
Contributor(s) Rizzardi LF, Hickey P, Hansen KD, Feinberg AP
Citation(s) 30643296
Submission date Mar 14, 2017
Last update date May 15, 2019
Contact name Andrew P. Feinberg
Organization name Johns Hopkins University School of Medicine
Street address 855 N. Wolfe St
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (20)
GSM2536613 5540_BA9_neg (RNA-Seq)
GSM2536614 5540_BA9_pos (RNA-Seq)
GSM2536615 5540_NAcc_neg (RNA-Seq)
This SubSeries is part of SuperSeries:
GSE96615 Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability
Relations
BioProject PRJNA379175
SRA SRP101890

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Supplementary file Size Download File type/resource
GSE96613_flow_sorted_brain.RNA-seq_gene_level_scaled_counts.txt.gz 9.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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