NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE185862 Query DataSets for GSE185862
Status Public on Oct 20, 2021
Title A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion and learning. We profiled ~1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic celltype taxonomy which includes many new glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and isocortex share a common circuit organization. We also identify large-scale continuous and graded variation of cell types along isocortical depth, across isocortical sheet and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity and function of these two brain structures.
 
Overall design Single cell RNA-seq using the 10x genomics and Smart-seq v4 methods. Cells were isolated from mouse cortex and hippocampal formation. The dataset includes 175 10x genomics libraries containing ~1.2 million cells and 73.363 Smart-seq v4 cells.
 
Contributor(s) Yao Z, van Velthoven CT, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding S, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H
Citation(s) 34004146
Submission date Oct 13, 2021
Last update date Dec 03, 2021
Contact name Hongkui Zeng
E-mail(s) hongkuiz@alleninstitute.org
Organization name Allen Institute for Brain Science
Street address 615 Westlake Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (95)
GSM5629156 Mouse 10x MOp
GSM5629157 Mouse 10x VISm
GSM5629158 Mouse 10x VISp
Relations
BioProject PRJNA772116
SRA SRP341866

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
GSE185862_CTX-HPF-73538sample_metadata.xlsx 13.2 Mb (ftp)(http) XLSX
GSE185862_CTX_HPF_2021_10x_readme.txt 1.9 Kb (ftp)(http) TXT
GSE185862_CTX_HPF_2021_SS_readme.txt 1.9 Kb (ftp)(http) TXT
GSE185862_expression_matrix_10x.hdf5 5.3 Gb (ftp)(http) HDF5
GSE185862_expression_matrix_SSv4.hdf5 3.3 Gb (ftp)(http) HDF5
GSE185862_metadata_10x.csv.gz 30.1 Mb (ftp)(http) CSV
GSE185862_metadata_ssv4.csv.gz 2.1 Mb (ftp)(http) CSV
GSE185862_sample_group_mapping.csv.gz 229.7 Kb (ftp)(http) CSV
GSE185862_umap.2d.10x.csv.gz 20.8 Mb (ftp)(http) CSV
GSE185862_umap2d_ssv4.csv.gz 1.1 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap