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| Status |
Public on Sep 08, 2021 |
| Title |
Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans |
| Organisms |
Macaca fascicularis; Macaca nemestrina; Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Abundant evidence supports the presence of at least three distinct types of thalamocortical (TC) neurons in the primate dorsal lateral geniculate nucleus (dLGN) of the thalamus, the brain region that conveys visual information from the retina to the primary visual cortex (V1). Different types of TC neurons in mice, humans, and macaques have distinct morphologies, distinct connectivity patterns, and convey different aspects of visual information to the cortex. To investigate the molecular underpinnings of these cell types, and how these relate to differences in dLGN between human, macaque, and mice, we profiled gene expression in single nuclei and cells using RNA-sequencing. These efforts identified four distinct types of TC neurons in the primate dLGN: magnocellular (M) neurons, parvocellular (P) neurons, and two types of koniocellular (K) neurons. Despite extensively documented morphological and physiological differences between M and P neurons, we identified few genes with significant differential expression between transcriptomic cell types corresponding to these two neuronal populations. Likewise, the dominant feature of TC neurons of the adult mouse dLGN is high transcriptomic similarity, with an axis of heterogeneity that aligns with core vs. shell portions of mouse dLGN. Together, these data show that transcriptomic differences between principal cell types in the mature mammalian dLGN are subtle relative to the observed differences in morphology and cortical projection targets. Finally, alignment of transcriptome profiles across species highlights expanded diversity of GABAergic neurons in primate versus mouse dLGN and homologous types of TC neurons in primates that are distinct from TC neurons in mouse.
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| Overall design |
Single-cell RNA-seq data from mouse dLGN, LP, and LGv. Single-nucleus RNA-seq data from Macaque dLGN and pulvinar. Single-cell RNA-seq data from human.
>>> Submitter declares that the human raw data will be deposited in dbGaP due to patient privacy concerns. <<<
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| Contributor(s) |
Bakken TE, van Velthoven CT, Menon V, Hodge RD, Yao Z, Nguyen TN, Graybuck LT, Horwitz GD, Bertagnolli D, Goldy J, Yanny A, Garren E, Parry S, Casper T, Shehata SI, Barkan ER, Szafer A, Levi BP, Dee N, Smith KA, Sunkin SM, Bernard A, Phillips J, Hawrylycz MJ, Koch C, Murphy GJ, Lein E, Zeng H, Tasic B |
| Citation(s) |
34473054 |
| Submission date |
Aug 16, 2021 |
| Last update date |
Sep 21, 2021 |
| Contact name |
Bosiljka Tasic |
| E-mail(s) |
bosiljkat@alleninstitute.org
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| Organization name |
Allen Institute for Brain Science
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| Department |
Molecular Genetics
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| Lab |
Tasic
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| Street address |
615 Westlake Ave N.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
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| Platforms (4)
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| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19597 |
Illumina HiSeq 2500 (Macaca nemestrina) |
| GPL20302 |
Illumina HiSeq 2500 (Macaca fascicularis) |
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| Samples (5552)
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| Relations |
| BioProject |
PRJNA755316 |
| SRA |
SRP332736 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE182211_human_LGN_2021_exon-matrix.csv.gz |
13.2 Mb |
(ftp)(http) |
CSV |
| GSE182211_human_LGN_2021_intron-matrix.csv.gz |
13.6 Mb |
(ftp)(http) |
CSV |
| GSE182211_human_LGN_2021_metadata.csv.gz |
137.0 Kb |
(ftp)(http) |
CSV |
| GSE182211_human_LGN_2021_readme.txt |
3.2 Kb |
(ftp)(http) |
TXT |
| GSE182211_macaque_LGN_2021_exon-matrix.csv.gz |
19.2 Mb |
(ftp)(http) |
CSV |
| GSE182211_macaque_LGN_2021_intron-matrix.csv.gz |
24.3 Mb |
(ftp)(http) |
CSV |
| GSE182211_macaque_LGN_2021_metadata.csv.gz |
222.4 Kb |
(ftp)(http) |
CSV |
| GSE182211_macaque_LGN_2021_readme.txt |
3.2 Kb |
(ftp)(http) |
TXT |
| GSE182211_mouse_LGN_2021_exon-matrix.csv.gz |
31.2 Mb |
(ftp)(http) |
CSV |
| GSE182211_mouse_LGN_2021_intron-matrix.csv.gz |
17.1 Mb |
(ftp)(http) |
CSV |
| GSE182211_mouse_LGN_2021_metadata.csv.gz |
210.8 Kb |
(ftp)(http) |
CSV |
| GSE182211_mouse_LGN_2021_readme.txt |
3.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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