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| 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
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| 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.
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| Overall design |
RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq for histone modifications using INTACT-purified nuclei from the mouse neocortex
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| 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 |
| E-mail(s) |
amo4@jhmi.edu
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| Phone |
410 955 4679
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| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Molecular Biology and Genetics
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| Lab |
Jeremy Nathans
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| Street address |
725 N. Wolfe St. PCTB805
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (31)
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| Relations |
| BioProject |
PRJNA266828 |
| SRA |
SRP049674 |
| 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) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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