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Series GSE130553 Query DataSets for GSE130553
Status Public on Aug 20, 2020
Title Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180226_1A]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in ~95,000 single nucleus from 38 mice rostral brain functional regions and structures (Apr. 2019). In each major brain regions (isocortex, striatum, pallidum, hippocampus, and olfactory bulb), we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the rostral mouse brain and the underlining regulatory epigenomic basis.
 
Overall design Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain
This submission consists of brain region (MOs).
 
Contributor(s) Liu H, Luo C, Rivkin A, Bartlett A, Lucero J, Nery JR, Aldridge A, Castanon R, He Y, Chen H, Zhang Z, Zhou J, Ren B, Mukamel EA, Behrens MM, Ecker JR
Citation(s) 34616061
Submission date May 01, 2019
Last update date Oct 15, 2021
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (1367)
GSM3742106 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD001_indexed
GSM3742107 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD004_indexed
GSM3742108 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD010_indexed
Relations
BioProject PRJNA540609
SRA SRP194377

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
GSE130553_RAW.tar 190.0 Gb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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