NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE150170 Query DataSets for GSE150170
Status Public on Nov 16, 2020
Title Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Neuronal cell types are classically defined by their molecular properties, anatomy, and functions. While recent advances in single-cell genomics have led to high-resolution molecular characterization of cell type diversity in the brain, neuronal cell types are often studied out of the context of their anatomical properties. To better understand the relationship between molecular and anatomical features defining cortical neurons, we developed Epi-Retro-Seq, a method that combined retrograde labeling with single-nucleus DNA methylation sequencing to link epigenomic properties of cell types to neuronal projections. We profiled 16,971 single neocortical neurons from 63 cortico-cortical and cortico-subcortical long-distance projections. Our results revealed unique epigenetic signatures of projection neurons that correspond to their laminar and regional location and projection patterns. The methylomes of 16,971 mouse neocortical neurons from 63 cortico-cortical (CC) and cortico-subcortical long-distance projections were analyzed using Epi-Retro-Seq, a method that combined retrograde tracing and single nucleus methylome sequencing.
 
Overall design In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from at least 4 mice (2 male and 2 female) for each projection target (except AI→pons - 2 male mice only). Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2 to profile their genome-wide DNA methylation signatures. We assayed approximately 384 nuclei from each projection (except the MOp→SSp projection from which 768 nuclei were assayed). Low-quality nuclei were removed.
 
Contributor(s) Zhang Z, Zhou J, Tan P, Pang Y, Rivkin A, Williams E, Lee C, A. Miyazaki P, Bartlett A, Aldridge A, Vu M, Boggeman L, Fitzpatrick C, Nery JR, Castanon RG, Rashid M, Jacobs M, Ito T, Dominguez B, Smith JB, O'Connor C, Lee K, Jin X, Mukamel EA, Behrens MM, Ecker JR, Callaway EM
Citation(s) 34616065
Submission date May 08, 2020
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
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (16971)
GSM4525612 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD001
GSM4525613 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD002
GSM4525614 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD004
Relations
BioProject PRJNA631508
SRA SRP261073

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
GSE150170_RAW.tar 2.2 Tb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap