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| Status |
Public on Dec 27, 2021 |
| Title |
Vision-dependent specification of cell types and function in the developing cortex |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The role of postnatal experience in sculpting cortical circuitry, while long appreciated, is poorly understood at the level of cell types. We explore this in the mouse primary visual cortex (V1) using single-nucleus RNA-sequencing, visual deprivation, genetics, and functional imaging. We find that vision selectively drives the specification of glutamatergic cell types in upper layers (L) (L2/3/4), while deeper-layer glutamatergic, GABAergic, and non-neuronal cell types are established prior to eye opening. L2/3 cell types form an experience-dependent spatial continuum defined by the graded expression of ~200 genes, including regulators of cell adhesion and synapse formation. One of these, Igsf9b, a vision-dependent gene encoding an inhibitory synaptic cell adhesion molecule, is required for the normal development of binocular responses in L2/3. In summary, vision preferentially regulates the development of upper-layer glutamatergic cell types through the regulation of cell type-specific gene expression programs.
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| Overall design |
Single-nucleus transcriptomics of P8, P14, P17, P21, P28, and P38 normally reared mice and P28 dark-reared, P38 dark-reared, and P28 dark-light reared mice. Each of the nine datasets was obtained from 30 mice.
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| Contributor(s) |
Cheng S, Butrus S, Tan L, Xu V, Sagireddy S, Trachtenberg J, Shekhar K, Zipursky SL |
| Citation(s) |
35063073, 38187533 |
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| Submission date |
Dec 14, 2021 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Salwan Butrus |
| E-mail(s) |
salwan@berkeley.edu
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| Organization name |
UC Berkeley
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| Department |
Chemical and Biomolecular Engineering
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| Lab |
Karthik Shekhar
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| Street address |
Stanley Hall Rm
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| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (35)
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| Relations |
| BioProject |
PRJNA788967 |
| SRA |
SRP351309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190940_P14NR.csv.gz |
183.8 Mb |
(ftp)(http) |
CSV |
| GSE190940_P17NR.csv.gz |
136.5 Mb |
(ftp)(http) |
CSV |
| GSE190940_P21NR.csv.gz |
113.7 Mb |
(ftp)(http) |
CSV |
| GSE190940_P28DL.csv.gz |
159.0 Mb |
(ftp)(http) |
CSV |
| GSE190940_P28DR.csv.gz |
174.9 Mb |
(ftp)(http) |
CSV |
| GSE190940_P28NR.csv.gz |
143.3 Mb |
(ftp)(http) |
CSV |
| GSE190940_P38DR.csv.gz |
165.6 Mb |
(ftp)(http) |
CSV |
| GSE190940_P38NR.csv.gz |
112.8 Mb |
(ftp)(http) |
CSV |
| GSE190940_P8NR.csv.gz |
102.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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