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Series GSE63137 Query DataSets for GSE63137
Status Public on Jun 17, 2015
Title Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary We developed an affinity purification approach to isolate tagged nuclei in mice (similar to INTACT; [Deal R.B. and Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 18,1030-1040. (2010)]) and used it to characterize genome-wide patterns of transcription, DNA methylation, and chromatin accessibility in 3 major neuron classes of the neocortex (excitatory pyramidal neurons, parvalbumin (PV)-positive GABAergic interneurons, and vasoactive intestinal peptide (VIP)-positive GABAergic interneurons). By combining cell purification and integrative analysis, our findings relate the phenotypic and functional complexity of neocortical neurons to their underlying transcriptional and epigenetic diversity.
Overall design RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq for histone modifications using INTACT-purified nuclei from the mouse neocortex
Contributor(s) Mo A, Mukamel EA, Davis FP, Luo C, Eddy SR, Ecker JR, Nathans J
Citation(s) 26087164
Submission date Nov 10, 2014
Last update date May 15, 2019
Contact name Alisa Mo
Phone 410 955 4679
Organization name Johns Hopkins University School of Medicine
Department Molecular Biology and Genetics
Lab Jeremy Nathans
Street address 725 N. Wolfe St. PCTB805
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (31)
GSM1541950 RNA-seq_excitatory_neurons_rep1
GSM1541951 RNA-seq_excitatory_neurons_rep2
GSM1541952 RNA-seq_PV_neurons_rep1
BioProject PRJNA266828
SRA SRP049674

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
GSE63137_ATAC-seq_PV_neurons_HOMER_peaks.bed.gz 835.3 Kb (ftp)(http) BED
GSE63137_ATAC-seq_VIP_neurons_HOMER_peaks.bed.gz 791.2 Kb (ftp)(http) BED
GSE63137_ATAC-seq_excitatory_neurons_HOMER_peaks.bed.gz 1.3 Mb (ftp)(http) BED
GSE63137_ChIP-seq_H3K27ac_excitatory_neurons_SICER_peaks.bed.gz 491.8 Kb (ftp)(http) BED
GSE63137_ChIP-seq_H3K27me3_excitatory_neurons_SICER_peaks.bed.gz 186.1 Kb (ftp)(http) BED
GSE63137_ChIP-seq_H3K4me1_excitatory_neurons_SICER_peaks.bed.gz 717.7 Kb (ftp)(http) BED
GSE63137_ChIP-seq_H3K4me3_excitatory_neurons_SICER_peaks.bed.gz 92.5 Kb (ftp)(http) BED
GSE63137_MethylC-seq_DMRs_methylpy.txt.gz 2.1 Mb (ftp)(http) TXT
GSE63137_MethylC-seq_PV_neurons_UMRs_LMRs.txt.gz 805.8 Kb (ftp)(http) TXT
GSE63137_MethylC-seq_VIP_neurons_UMRs_LMRs.txt.gz 786.6 Kb (ftp)(http) TXT
GSE63137_MethylC-seq_excitatory_neurons_UMRs_LMRs.txt.gz 1.1 Mb (ftp)(http) TXT
GSE63137_RAW.tar 31.6 Gb (http)(custom) TAR (of BW, TAR, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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