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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 10, 2021 |
| Title |
Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. [single whole-cell] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: While great progress has been made in understanding the differences in regional stem cell potential using viral and genetic lineage tracing strategies, the core molecular heterogeneity that underlies these regional differences is largely unknown.
Methods: Here we present a single whole-cell sequencing dataset of microdissected adult hGFAP:GFP mouse V-SVZ. Four samples were (two samples from male mice, two samples from female mice) multiplexed & combined using MULTI-Seq barcodes (McGinnes et al. 2019), labeled with TotalSeq antibodies against VCAM1 and CD24 proteins (Biolegend), and were split into two technical replicate lanes on a 10x Chromium Single Cell Controller chip for single cell barcoding. Genomic libraries were prepared using standard Illumina protocols, and barcode libraries (MULTI-Seq, TotalSeq) were prepared using MULTI-Seq protocols.
Results: Here we present single whole-cell and single nucleus sequencing datasets of microdissected adult mouse V-SVZ, and evidence for the existence of two broad subtypes of adult neural stem cells. By using spatially resolved microdissections in the single nucleus sequencing dataset as a reference, and mapping marker gene expression in the V-SVZ, we find that these two populations reside in largely non-overlapping domains in either the dorsal or ventral V-SVZ. Furthermore, we identified two subpopulations of newly born neurons that have gene expression consistent with dorsal or ventral origins. Finally, we identify genes expressed by both stem cells and the neurons they generate that specifically mark either the dorsal or ventral adult neurogenic lineage. These datasets, methods and findings will enable future study of region-specific regulation of adult neurogenesis.
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| Overall design |
Single cell profiles of micro-dissected ventricular-subventricular zones of male (postnatal day 35) and female (postnatal day 29) hGFP:GFP mice.
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| Contributor(s) |
Redmond SA, Cebrian Silla A, AssisNascimento M, Mansky B, Wu D, Obernier K, Romero Rodriguez R, Lim DA, Alvarez-Buylla A |
| Citation(s) |
34259628 |
| Submission date |
Jan 26, 2021 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Stephanie A Redmond |
| E-mail(s) |
stephanie.redmond@ucsf.edu
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| Organization name |
University of California San Francisco
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| Department |
Neurosurgery
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| Lab |
Arturo Alvarez-Buylla
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| Street address |
35 Medical Center Way, 933D Box 0525
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (1) |
| GSM5039270 |
mixed sample (non-demultiplexed); Male and Female |
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| This SubSeries is part of SuperSeries: |
| GSE165555 |
Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. |
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| Relations |
| BioProject |
PRJNA694959 |
| SRA |
SRP303345 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165554_RAW.tar |
2.3 Gb |
(http)(custom) |
TAR (of MTX, RDS, TSV) |
| GSE165554_readme.xlsx |
11.7 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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