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Series GSE213262

Query DataSets for GSE213262

Status

Public on Apr 13, 2023

Title

DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain

Project

CEMBA Epigenomic Landscape of Mouse Brain

Organism

Experiment type

Methylation profiling by high throughput sequencing
Other

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 117 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 117 brain functional regions to identify epigenomic landcape of the adult mouse brain.

This project includes the following series:
GSE213221 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213221
GSE213259 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213259
GSE213353 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213353
GSE215147 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215147
GSE215213 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215213
GSE215342 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215342
GSE215422 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215422
GSE215779 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215779
GSE215809 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215809
GSE215913 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215913
GSE215958 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215958
GSE215995 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215995
GSE216014 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216014
GSE216041 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216041
GSE216188 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216188
GSE216224 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216224
GSE216240 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216240
GSE216300 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216300
GSE216331 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216331
GSE216436 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216436
GSE230219 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230219
GSE230220 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230220
GSE230221 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230221
GSE230222 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230222
GSE230223 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230223
GSE230224 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230224
GSE230225 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230225
GSE230226 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230226
GSE230242 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230242
GSE230248 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230248
GSE230335 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230335
GSE230336 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230336
GSE230338 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230338
GSE230339 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230339
GSE232593 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232593
GSE232663 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232663
GSE232668 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232668
GSE232768 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232768
GSE232909 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232909
GSE232945 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232945
GSE233185 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233185
GSE233268 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233268
GSE234950 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234950
GSE235004 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235004
GSE236274 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236274
GSE236428 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236428
GSE236451 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236451
GSE236574 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236574
GSE236583 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236583
GSE236612 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236612
GSE236699 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236699
GSE236893 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236893
GSE236973 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236973
GSE237288 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237288
GSE237325 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237325
GSE237437 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237437
GSE237455 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237455
GSE237580 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237580
GSE237699 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237699
GSE237781 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237781

Contributor(s)

Liu H, Bartlett A, Lucero J, Osteen JK, Altshul J, Kenworthy M, Castanon RG, Nery JR, Berube P, Chen H, Nunn M, Dixon JR, Behrens MM, Ecker JR

Citation(s)

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
HHMI_Ecker_J	Investigator	Ecker, Joseph R.	Joseph R. Ecker

Submission date

Sep 13, 2022

Last update date

Jul 20, 2023

Contact name

Joseph R Ecker

E-mail(s)

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)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary data files not provided

Processed data provided as supplementary file

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