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Series GSE107638 Query DataSets for GSE107638
Status Public on Jun 25, 2019
Title Contribution of differential cell-specific methylation to schizophrenia [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To address the heterogeneity of gene regulation and expression in cell types of a brain region with strong evidence for relevance to schizophrenia, we carried out whole genome methylation and expression analyses using post-mortem brain tissue from BA46 that underwent fluorescence-activated nuclei sorting (FANS). Importantly, we used whole genome bisulfite sequencing (WGBS) for methylation quantification to have an unbiased assessment of epigenetic modifications associated with schizophrenia, and additionally carried out whole genome sequencing (WGS) of the brain samples to account for genetic background differences. We found that a number of schizophrenia GWAS loci overlap with sites of cell-specific differential methylation in schizophrenia brain tissue. Differential methylation is also associated with differential gene expression in a cell-specific manner. Co-expression network analysis can identify groups of genes that are enriched for differentially methylated regions in each cell type, and these groups of co-expressed genes underscore shared molecular pathways that might be at risk in schizophrenia. Together, these data indicate that the integration of multiple levels of data in a cell-specific manner can provide novel biological insights into complex genetic disorders such as schizophrenia.
 
Overall design We carried out RNA-sequencing (RNA-seq) of NeuN and OLIG2 positive nuclei from Brodmann area 46 of schizophrenia and matched controls of adult human neocortex.
 
Contributor(s) Berto S, Usui N, Toriumi K, Douglas C, Konopka G
Citation(s) 31288836
Submission date Dec 04, 2017
Last update date Nov 15, 2019
Contact name Genevieve Konopka
E-mail(s) gena@alum.mit.edu
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (96)
GSM2873928 1505_Schizo_NeuN
GSM2873929 1506_Schizo_NeuN
GSM2873930 1507_Schizo_NeuN
This SubSeries is part of SuperSeries:
GSE108066 Contribution of differential cell-specific methylation to schizophrenia
Relations
BioProject PRJNA420952
SRA SRP126056

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE107638_COUNTS_Cyto.txt.gz 210.3 Kb (ftp)(http) TXT
GSE107638_COUNTS_Exons_NeuN.txt.gz 1015.9 Kb (ftp)(http) TXT
GSE107638_COUNTS_Exons_OLIG2.txt.gz 836.5 Kb (ftp)(http) TXT
GSE107638_Demographics_NeuN.txt.gz 780 b (ftp)(http) TXT
GSE107638_Demographics_OLIG2.txt.gz 658 b (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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