Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain

Abstract
Data availability
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Abstract

The ventricular zone (VZ) of the nervous system contains radial glia cells that were originally considered relatively homogenous in their gene expression, but a detailed characterization of transcriptional diversity in these VZ cells has not been reported. Here, we performed single-cell RNA sequencing to characterize transcriptional heterogeneity of neural progenitors within the VZ and subventricular zone (SVZ) of the ganglionic eminences (GEs), the source of all forebrain GABAergic neurons. By using a transgenic mouse line to enrich for VZ cells, we characterize significant transcriptional heterogeneity, both between GEs and within spatial subdomains of specific GEs. Additionally, we observe differential gene expression between E12.5 and E14.5 VZ cells, which could provide insights into temporal changes in cell fate. Together, our results reveal a previously unknown spatial and temporal genetic diversity of VZ cells in the ventral forebrain that will aid our understanding of initial fate decisions in the forebrain.

Data availability

All of our sequencing data has been deposited in GEO under accession code GSE167013 and GSE190593.

The following data sets were generated

1. Lee DR
2. Rhodes CT
3. Mitra A
4. Zhang Y
5. Maric D
6. Dale RK
7. Petros TJ
(2021) Transcriptional heterogeneity of ventricular zone cells throughout the embryonic mouse forebrain
NCBI Gene Expression Omnibus, GSE167013.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167013
1. Lee DR
2. Rhodes CT
3. Mitra A
4. Zhang Y
5. Maric D
6. Dale RK
7. Petros TJ
(2021) Transcriptional heterogeneity of ventricular zone cells throughout the embryonic mouse forebrain
NCBI Gene Expression Omnibus, GSE190593.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190593

The following previously published data sets were used

1. Mayer
2. C
3. Hafemeister
4. C
5. Bandler
6. RC
7. Machold
8. R
9. Batista Brito
10. R
11. Jaglin
12. X
13. Allaway
14. K
15. Butler
16. A
17. Fishell
18. G
19. and Satija
20. R
(2018) Developmental diversification of cortical inhibitory interneurons
NCBI Gene Expression Omnibus, GSE103983.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103983
1. Mi
2. D
3. Li
4. Z
5. Lim
6. L
7. Li
8. M
9. Moissidis
10. M
11. Yang
12. Y
13. Gao
14. T
15. Hu
16. TX
17. Pratt
18. T
19. Price
20. DJ
21. Sestan
22. N
23. Marin
24. O
(2018) Early emergence of cortical interneuron diversity in the mouse embryo
NCBI Gene Expression Omnibus, GSE109796.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109796

Article and author information

Author details

Dongjin R Lee

Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States

Competing interests
The authors declare that no competing interests exist.
Christopher Rhodes

Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7438-4236
Apratim Mitra

Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States

Competing interests
The authors declare that no competing interests exist.
Yajun Zhang

Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States

Competing interests
The authors declare that no competing interests exist.
Dragan Maric

Flow and Imaging Cytometry Core, National Institute of Neurological Disease and Stroke, Bethesda, United States

Competing interests
The authors declare that no competing interests exist.
Ryan K Dale

Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States

Competing interests
The authors declare that no competing interests exist.
Timothy J Petros

Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States

For correspondence
tim.petros@nih.gov

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8943-546X

Funding

Eunice Kennedy Shriver National Institute of Child Health and Human Development (Intramural Award)

Timothy J Petros

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mouse colonies were maintained in accordance with protocols approved by the Animal Care and Use Committee at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) under animal study protocol ASP #20-047.

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.