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Series GSE132489 Query DataSets for GSE132489
Status Public on Oct 06, 2021
Title DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution
Project CEMBA Epigenomic Landscape of Mouse Brain
Sample 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 (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.
 
Overall design 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 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134653
GSE134750 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134750
GSE134773 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134773
GSE134793 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134793
GSE134806 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134806
GSE134862 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134862
GSE134882 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134882
GSE134899 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134899
GSE134940 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134940
GSE134958 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134958
GSE134967 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134967
GSE135139 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135139
GSE135169 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135169
GSE135179 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135179
GSE135203 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
Web link http://neomorph.salk.edu/omb
 
Contributor(s) Liu H, Bartlett A, Aldridge A, Luo C, Lucero J, Nery JR, Osteen JK, Zhou J, Tian W, Chen H, Rivkin A, Castanon RG, Pinto-Duarte A, O'Connor C, Boggeman L, Fitzpatrick C, Behrens M, Ecker JR
Citation(s) 34616061
NIH grant(s)
Grant ID Grant title Affiliation Name
U19 MH114831 Center for Epigenomics of the Mouse Brain Atlas (CEMBA) THE SALK INSTITUTE FOR BIOLOGICAL STUDIES Joseph R Ecker
R01 HG010634 Development of methods for multi-omic analysis of DNA methylation and chromatin architecture in single cells THE SALK INSTITUTE FOR BIOLOGICAL STUDIES Joseph R Ecker
Submission date Jun 10, 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
 

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
GSE132489_10E-190625.mcds.hdf5 959.2 Mb (ftp)(http) HDF5
GSE132489_10E-190627.mcds.hdf5 943.4 Mb (ftp)(http) HDF5
GSE132489_10F-190625.mcds.hdf5 976.8 Mb (ftp)(http) HDF5
GSE132489_10F-190627.mcds.hdf5 975.6 Mb (ftp)(http) HDF5
GSE132489_11E-190214.mcds.hdf5 880.2 Mb (ftp)(http) HDF5
GSE132489_11E-190305.mcds.hdf5 913.1 Mb (ftp)(http) HDF5
GSE132489_11F-190214.mcds.hdf5 918.1 Mb (ftp)(http) HDF5
GSE132489_11F-190305.mcds.hdf5 904.9 Mb (ftp)(http) HDF5
GSE132489_1A-180226.mcds.hdf5 870.8 Mb (ftp)(http) HDF5
GSE132489_1A-180227.mcds.hdf5 702.8 Mb (ftp)(http) HDF5
GSE132489_1B-180119.mcds.hdf5 913.7 Mb (ftp)(http) HDF5
GSE132489_1B-180213.mcds.hdf5 894.1 Mb (ftp)(http) HDF5
GSE132489_1C-180208.mcds.hdf5 880.9 Mb (ftp)(http) HDF5
GSE132489_1C-180212.mcds.hdf5 807.0 Mb (ftp)(http) HDF5
GSE132489_2A-180122.mcds.hdf5 745.7 Mb (ftp)(http) HDF5
GSE132489_2A-180123.mcds.hdf5 890.3 Mb (ftp)(http) HDF5
GSE132489_2B-180305.mcds.hdf5 664.3 Mb (ftp)(http) HDF5
GSE132489_2B-180306.mcds.hdf5 904.2 Mb (ftp)(http) HDF5
GSE132489_2C-180409.mcds.hdf5 739.4 Mb (ftp)(http) HDF5
GSE132489_2C-180410.mcds.hdf5 673.8 Mb (ftp)(http) HDF5
GSE132489_2D-180313.mcds.hdf5 351.1 Mb (ftp)(http) HDF5
GSE132489_2D-180319.mcds.hdf5 205.9 Mb (ftp)(http) HDF5
GSE132489_2D-180403.mcds.hdf5 1023.6 Mb (ftp)(http) HDF5
GSE132489_2E-180220.mcds.hdf5 920.0 Mb (ftp)(http) HDF5
GSE132489_2E-180222.mcds.hdf5 798.8 Mb (ftp)(http) HDF5
GSE132489_3A-180129.mcds.hdf5 882.1 Mb (ftp)(http) HDF5
GSE132489_3A-180130.mcds.hdf5 822.8 Mb (ftp)(http) HDF5
GSE132489_3B-180312.mcds.hdf5 855.6 Mb (ftp)(http) HDF5
GSE132489_3B-180501.mcds.hdf5 725.5 Mb (ftp)(http) HDF5
GSE132489_3C-171206.mcds.hdf5 766.6 Mb (ftp)(http) HDF5
GSE132489_3C-171207.mcds.hdf5 810.2 Mb (ftp)(http) HDF5
GSE132489_3D-180412.mcds.hdf5 711.6 Mb (ftp)(http) HDF5
GSE132489_3D-180416.mcds.hdf5 824.7 Mb (ftp)(http) HDF5
GSE132489_3E-180320.mcds.hdf5 853.1 Mb (ftp)(http) HDF5
GSE132489_3E-180326.mcds.hdf5 759.6 Mb (ftp)(http) HDF5
GSE132489_3F-180109.mcds.hdf5 676.3 Mb (ftp)(http) HDF5
GSE132489_3F-180405.mcds.hdf5 726.2 Mb (ftp)(http) HDF5
GSE132489_4A-180205.mcds.hdf5 759.0 Mb (ftp)(http) HDF5
GSE132489_4A-180206.mcds.hdf5 829.7 Mb (ftp)(http) HDF5
GSE132489_4B-171212.mcds.hdf5 194.5 Mb (ftp)(http) HDF5
GSE132489_4B-171213.mcds.hdf5 804.5 Mb (ftp)(http) HDF5
GSE132489_4B-180104.mcds.hdf5 843.0 Mb (ftp)(http) HDF5
GSE132489_4C-180417.mcds.hdf5 670.6 Mb (ftp)(http) HDF5
GSE132489_4C-180419.mcds.hdf5 642.2 Mb (ftp)(http) HDF5
GSE132489_4D-171214.mcds.hdf5 706.0 Mb (ftp)(http) HDF5
GSE132489_4D-171219.mcds.hdf5 912.4 Mb (ftp)(http) HDF5
GSE132489_4E-180110.mcds.hdf5 780.5 Mb (ftp)(http) HDF5
GSE132489_4E-180111.mcds.hdf5 348.6 Mb (ftp)(http) HDF5
GSE132489_4F-180329.mcds.hdf5 855.6 Mb (ftp)(http) HDF5
GSE132489_4F-180402.mcds.hdf5 802.6 Mb (ftp)(http) HDF5
GSE132489_4G-180917.mcds.hdf5 681.3 Mb (ftp)(http) HDF5
GSE132489_4G-181204.mcds.hdf5 660.5 Mb (ftp)(http) HDF5
GSE132489_4H-180724.mcds.hdf5 125.1 Mb (ftp)(http) HDF5
GSE132489_4H-180806.mcds.hdf5 460.3 Mb (ftp)(http) HDF5
GSE132489_4H-180911.mcds.hdf5 777.3 Mb (ftp)(http) HDF5
GSE132489_5A-190205.mcds.hdf5 909.3 Mb (ftp)(http) HDF5
GSE132489_5A-190307.mcds.hdf5 819.6 Mb (ftp)(http) HDF5
GSE132489_5B-180514.mcds.hdf5 544.3 Mb (ftp)(http) HDF5
GSE132489_5B-180529.mcds.hdf5 767.2 Mb (ftp)(http) HDF5
GSE132489_5C-181002.mcds.hdf5 803.2 Mb (ftp)(http) HDF5
GSE132489_5C-181210.mcds.hdf5 863.8 Mb (ftp)(http) HDF5
GSE132489_5D-180605.mcds.hdf5 728.1 Mb (ftp)(http) HDF5
GSE132489_5D-180612.mcds.hdf5 785.5 Mb (ftp)(http) HDF5
GSE132489_5E-180925.mcds.hdf5 914.3 Mb (ftp)(http) HDF5
GSE132489_5E-181206.mcds.hdf5 815.2 Mb (ftp)(http) HDF5
GSE132489_5F-181218.mcds.hdf5 562.6 Mb (ftp)(http) HDF5
GSE132489_5F-181220.mcds.hdf5 1.1 Gb (ftp)(http) HDF5
GSE132489_5G-181008.mcds.hdf5 894.7 Mb (ftp)(http) HDF5
GSE132489_5G-181009.mcds.hdf5 884.0 Mb (ftp)(http) HDF5
GSE132489_5H-181015.mcds.hdf5 908.6 Mb (ftp)(http) HDF5
GSE132489_5H-181016.mcds.hdf5 870.1 Mb (ftp)(http) HDF5
GSE132489_5J-190207.mcds.hdf5 877.1 Mb (ftp)(http) HDF5
GSE132489_6A-190108.mcds.hdf5 912.4 Mb (ftp)(http) HDF5
GSE132489_6A-190117.mcds.hdf5 876.5 Mb (ftp)(http) HDF5
GSE132489_6B-181022.mcds.hdf5 873.3 Mb (ftp)(http) HDF5
GSE132489_6B-181023.mcds.hdf5 882.8 Mb (ftp)(http) HDF5
GSE132489_6C-190122.mcds.hdf5 866.3 Mb (ftp)(http) HDF5
GSE132489_6C-190124.mcds.hdf5 810.2 Mb (ftp)(http) HDF5
GSE132489_6D-190131.mcds.hdf5 844.9 Mb (ftp)(http) HDF5
GSE132489_6D-190205.mcds.hdf5 911.8 Mb (ftp)(http) HDF5
GSE132489_7B-180423.mcds.hdf5 795.0 Mb (ftp)(http) HDF5
GSE132489_7B-180424.mcds.hdf5 588.5 Mb (ftp)(http) HDF5
GSE132489_8B-180426.mcds.hdf5 840.4 Mb (ftp)(http) HDF5
GSE132489_8B-180430.mcds.hdf5 819.0 Mb (ftp)(http) HDF5
GSE132489_8E-190711.mcds.hdf5 965.5 Mb (ftp)(http) HDF5
GSE132489_8E-190716.mcds.hdf5 967.4 Mb (ftp)(http) HDF5
GSE132489_8J-190711.mcds.hdf5 954.7 Mb (ftp)(http) HDF5
GSE132489_8J-190716.mcds.hdf5 951.0 Mb (ftp)(http) HDF5
GSE132489_9H-190212.mcds.hdf5 796.9 Mb (ftp)(http) HDF5
GSE132489_9H-190219.mcds.hdf5 894.1 Mb (ftp)(http) HDF5
GSE132489_9J-190212.mcds.hdf5 924.4 Mb (ftp)(http) HDF5
GSE132489_9J-190219.mcds.hdf5 864.5 Mb (ftp)(http) HDF5
GSE132489_GEOaccession_with_CEMBA_ID.txt.gz 699 b (ftp)(http) TXT
GSE132489_MCDS_FILES_README.txt 1.2 Kb (ftp)(http) TXT
Processed data provided as supplementary file
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