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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
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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.
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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.
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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 |
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Submission date |
Oct 13, 2021 |
Last update date |
Dec 03, 2021 |
Contact name |
Hongkui Zeng |
E-mail(s) |
hongkuiz@alleninstitute.org
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Organization name |
Allen Institute for Brain Science
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Street address |
615 Westlake Ave N
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98109 |
Country |
USA |
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Platforms (2) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (95)
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Relations |
BioProject |
PRJNA772116 |
SRA |
SRP341866 |
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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