DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

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 (45 in the current release) brain functional 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. Apply snmC-seq2 to brain functional regions to identify the epigenomic landscape of the adult mouse brain. The file GSE132489_GEOaccession_with_CEMBA_ID.txt.gz, available at the foot of this record contains all included GSE ID with associated CEMBA ID. This project includes the following series: GSE130553 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130553 GSE131192 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131192 GSE131326 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131326 GSE131354 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131354 GSE131360 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131360 GSE131393 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131393 GSE131406 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131406 GSE131427 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131427 GSE131430 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131430 GSE131501 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131501 GSE131509 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131509 GSE131519 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131519 GSE131554 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131554 GSE131557 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131557 GSE131570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131570 GSE131757 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131757 GSE131766 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131766 GSE131771 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131771 GSE131836 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131836 GSE131867 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131867 GSE131889 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131889 GSE131904 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131904 GSE131913 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131913 GSE131930 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131930 GSE131951 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131951 GSE132060 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132060 GSE132101 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132101 GSE132114 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132114 GSE132126 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132126 GSE132135 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132135 GSE132405 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132405 GSE132445 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132445 GSE132456 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132456 GSE132463 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132463 GSE132484 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132484 GSE132498 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132498 GSE132503 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132503 GSE132541 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132541 GSE132571 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132571 GSE132601 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132601 GSE132609 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132609 GSE132621 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132621 GSE132629 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132629 GSE132639 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132639 GSE132676 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132676 GSE132692 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132692 GSE132700 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132700 GSE132710 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132710 GSE134474 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134474 GSE134484 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134484 GSE134490 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134490 GSE134507 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134507 GSE134593 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134593 GSE134617 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134617 GSE134635 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134635 GSE134653 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https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135203 GSE135234 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135234 GSE135248 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135248 GSE135252 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135252 GSE135260 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135260 GSE135269 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135269 GSE135307 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135307 GSE135447 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135447 GSE135484 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135484 GSE135534 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135534 GSE135543 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135543 GSE135570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135570 GSE135585 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135585 GSE135596 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135596 GSE135606 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135606 GSE135641 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135641 GSE156683 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156683 GSE157868 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157868 GSE157886 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157886 GSE157980 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157980 GSE158014 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158014 GSE158043 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158043 GSE158066 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158066 GSE158092 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158092 GSE158154 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158154