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Series GSE138100 Query DataSets for GSE138100
Status Public on Dec 06, 2019
Title Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.
Overall design DNA methylation (RRBS) and gene expression (mRNA-seq) changes in neurons and glia; Right hippocampus of kainic acid injected mice (numbner of mice=8, number of samples=3); vs saline injected mice(numbner of mice=8, number of samples=3) at 24 hrs post injection.
Contributor(s) Hjorthaug HS, Vigeland MD, Nome CG, Berger TC, Etholm L, Taubøll E, Heuser K, Selmer KK
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Submission date Sep 27, 2019
Last update date Dec 08, 2019
Contact name Magnus D. Vigeland
Organization name University of Oslo
Department Medical Genetics
Street address Kirkeveien 166
City Oslo
ZIP/Postal code 0424
Country Norway
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (24)
GSM4099304 KRn_1_RRBS
GSM4099305 KRp_1_RRBS
GSM4099306 SRn_1_RRBS
BioProject PRJNA574618
SRA SRP223512

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE138100_RAW.tar 167.6 Mb (http)(custom) TAR (of COV)
GSE138100_counts_gencode.M16.txt.gz 998.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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