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Series GSE134617 Query DataSets for GSE134617
Status Public on Sep 09, 2020
Title Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180911_4H]
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 118 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, 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 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 subseries consists of one single nucleus methylation sequencing experiment of brain region (PAL).
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 Jul 22, 2019
Last update date Oct 15, 2021
Contact name Joseph R Ecker
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 (1221)
GSM3958189 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A11_AD012_indexed
GSM3958190 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD001_indexed
GSM3958191 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_A10_AD002_indexed
BioProject PRJNA555890
SRA SRP215888

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Supplementary file Size Download File type/resource
GSE134617_RAW.tar 183.1 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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