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Series GSE125068 Query DataSets for GSE125068
Status Public on Sep 03, 2019
Title Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Activity-driven transcription plays an important role in many brain processes, including those underlying memory and epilepsy. Here, we combine genetic tagging of nuclei and ribosomes with RNA-seq, ChIP-seq, ATAC-seq and Hi-C to investigate transcriptional and chromatin changes occurring in mouse hippocampal excitatory neurons at different timepoints after synchronous activation during seizure and sparse activation by novel context exploration. The transcriptional burst is associated with an increase in chromatin accessibility of activity-regulated genes and enhancers, de novo binding of activity-regulated transcription factors, augmented promoter-enhancer interactions, and the formation of gene loops that bring together the TSS and TTS of induced genes and may sustain the fast re-loading of RNAPII complexes. Some chromatin occupancy changes and interactions, particularly those driven by AP1, remain long after neuronal activation and could underlie the changes in neuronal responsiveness and circuit connectivity observed in these neuroplasticity paradigms, perhaps thereby contributing to metaplasticity in the adult brain.
Overall design nuRNA-seq, riboRNA-seq, ATAC-seq, ChIP-seq and HiC in mouse adult hippocampal excitatory neurons
Contributor(s) Fernandez-Albert J, López-Cascales MT, Barco Guerrero AL
Citation(s) 31501571
Submission date Jan 14, 2019
Last update date Dec 03, 2019
Contact name Angel Barco
Organization name Instituto de Neurociencias (UMH-CSIC)
Street address Av. Santiago Ramón y Cajal
City Sant Joan d'Alacant
State/province Alicante
ZIP/Postal code 03550
Country Spain
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (40)
GSM3562094 riboRNA_Sal_rep1
GSM3562095 riboRNA_Sal_rep2
GSM3562096 riboRNA_Sal_rep3
BioProject PRJNA515067
SRA SRP179090

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
GSE125068_ATACseq.tar.gz 4.2 Gb (ftp)(http) TAR
GSE125068_ChIPseq.tar.gz 1.4 Gb (ftp)(http) TAR
GSE125068_HiC.tar.gz 5.4 Gb (ftp)(http) TAR
GSE125068_nuRNAseq.tar.gz 929.4 Mb (ftp)(http) TAR
GSE125068_riboseq.tar.gz 45.8 Mb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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