| Field |
Value |
| Identifier |
nemo:dat-tfmg0va |
| Dataset Name |
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 |
| Version |
NA |
| Release Date |
NA |
| DOI |
NA |
| Source Data URL |
|
| Dataset Collection URL |
https://data.nemoarchive.org/publication_release/Bakken_2021_dLGN_CrossSpecies_Rseq.tgz |
| Description |
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. |
| Keywords |
scRNA-seq, Smart-seq v4, dLGN |
| Total Files in Collection |
5585 |
| Total Size in Collection (in GB) |
821.3 |
| Authors |
Trygve E Bakken, Cindy TJ van Velthoven, Vilas Menon, Rebecca D Hodge, Zizhen Yao, Thuc Nghi Nguyen, Lucas T Graybuck, Gregory D Horwitz, Darren Bertagnolli, Jeff Goldy, Anna Marie Yanny, Emma Garren, Sheana Parry, Tamara Casper, Soraya I Shehata, Eliza R Barkan, Aaron Szafer, Boaz P Levi, Nick Dee, Kimberly A Smith, Susan M Sunkin, Amy Bernard, John Phillips, Michael J Hawrylycz, Christof Koch, Gabe J Murphy, Ed Lein, Hongkui Zeng, Bosiljka Tasic |
| Organization |
Allen Institute for Brain Science |
| Contact Person |
Bosiljka Tasic |
| Contact E-Mail |
bosiljkat@alleninstitute.org |
| External Identifier |
https://doi.org/10.7554/eLife.64875 |
| Grant Name |
No external funding was received for this work |
| Consortium |
BICCN |
| Data Repository |
NeMO |
| Data Repository RRID |
RRID:SCR_016152 |
| Data License |
Public data available under CC BY 4.0; controlled access data subject to data use certification |
| Data Access |
https://biccn.org/terms-of-use |
| Community Standards |
https://biccn.org/standards |
| Study Organism |
human, mouse, macaque |
| Protocol ID |
dx.doi.org/10.17504/protocols.io.bq7dmzi6; dx.doi.org/10.17504/protocols.io.bq6ymzfw; dx.doi.org/10.17504/protocols.io.bf4ajqse |
