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SRX6033821: GSM3870431: 180508_CEMBA_mm_P56_P63_2C_CEMBA180409_2C_1_CEMBA180409_2C_2_G10_AD010_indexed; Mus musculus; OTHER
1 ILLUMINA (Illumina NovaSeq 6000) run: 3.2M spots, 947.5M bases, 333.7Mb downloads

Submitted by: NCBI (GEO)
Study: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180409_2C]
show Abstracthide Abstract
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 (MOp).
Sample: 180508_CEMBA_mm_P56_P63_2C_CEMBA180409_2C_1_CEMBA180409_2C_2_G10_AD010_indexed
SAMN12009788 • SRS4937388 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342. Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.
Experiment attributes:
GEO Accession: GSM3870431
Links:
Runs: 1 run, 3.2M spots, 947.5M bases, 333.7Mb
Run# of Spots# of BasesSizePublished
SRR92630653,225,408947.5M333.7Mb2020-08-26

ID:
8076263

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