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| Status |
Public on Nov 18, 2021 |
| Title |
Transcriptomic Taxonomy and Neurogenic Trajectories of Adult Human, Macaque and Pig Hippocampal and Entorhinal Cells |
| Organisms |
Macaca mulatta; Homo sapiens; Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The hippocampal-entorhinal system supports cognitive functions, has lifelong neurogenic capabilities in many species, and is selectively vulnerable to Alzheimer’s disease. To investigate neurogenic potential and cellular diversity, we profiled single-nucleus transcriptomes in five hippocampal-entorhinal subregions in human, macaque, and pig. Integrated cross-species analysis revealed robust transcriptomic and histologic signatures of neurogenesis in adult mouse, pig and macaque, but not humans. Doublecortin (DCX), a widely accepted marker of newly generated granule cells, was detected in diverse human neurons, but it did not define immature neuron populations. To explore species differences in cellular diversity and implications for disease, we characterized subregion-specific transcriptomically-defined cell types and transitional changes from the three-layered archicortex to the six-layered neocortex. Notably, METTL7B defined subregion-specific excitatory neurons and astrocytes in primates, associated with endoplasmic reticulum and lipid droplet proteins, including Alzheimer's disease-related proteins. Together this resource reveals cell-type- and species-specific properties shaping hippocampal-entorhinal neurogenesis and function.
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| Overall design |
snRNA-seq of hippocampal-entorhinal system in 6 human donors, dentate gyrus in 3 rhesus macaque donors, and adult hippocampus in 9 pig donors with different postmortem intervals (30 minutes, 1 hour, 7 hour)
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| Contributor(s) |
Franjic D, Skarica M, Ma S, Arellano JI, Tebbenkamp AT, Choi J, Xu C, Li Q, Morozov YM, Andrijevic D, Vrselja Z, Spajic A, Santpere G, Li M, Zhang S, Liu Y, Spurrier J, Zhang L, Gudelj I, Rapan L, Takahashi H, Huttner A, Fan R, Strittmatter SM, Sousa AM, Rakic P, Sestan N |
| Citation(s) |
34798047 |
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| Submission date |
Oct 25, 2021 |
| Last update date |
Feb 17, 2022 |
| Contact name |
Nenad Sestan |
| E-mail(s) |
nenad.sestan@yale.edu
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| Organization name |
Yale University
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| Department |
Neuroscience
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| Street address |
333 Cedar street
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| City |
New haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platforms (3) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL22475 |
Illumina HiSeq 4000 (Sus scrofa) |
| GPL23949 |
Illumina HiSeq 4000 (Macaca mulatta) |
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| Samples (50)
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| Relations |
| BioProject |
PRJNA774338 |
| SRA |
SRP343046 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186538_Human_cell_meta.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE186538_Human_counts.mtx.gz |
1.4 Gb |
(ftp)(http) |
MTX |
| GSE186538_Human_genes.txt.gz |
118.4 Kb |
(ftp)(http) |
TXT |
| GSE186538_Pig_cell_meta.txt.gz |
995.8 Kb |
(ftp)(http) |
TXT |
| GSE186538_Pig_counts.mtx.gz |
204.4 Mb |
(ftp)(http) |
MTX |
| GSE186538_Pig_genes.txt.gz |
103.0 Kb |
(ftp)(http) |
TXT |
| GSE186538_Rhesus_cell_meta.txt.gz |
811.8 Kb |
(ftp)(http) |
TXT |
| GSE186538_Rhesus_counts.mtx.gz |
163.9 Mb |
(ftp)(http) |
MTX |
| GSE186538_Rhesus_genes.txt.gz |
113.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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