Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. [single whole-cell]

Experiment ID:SRP303345
Technology:scRNA-Seq
Description: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. Overall design: Single cell profiles of micro-dissected ventricular-subventricular zones of male (postnatal day 35) and female (postnatal day 29) hGFP:GFP mice.
DOI:10.7554/eLife.67436
Source:SRP303345 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Mus musculusscRNA-Seq droplet-based H5AD data per cell in Mus musculus

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX9940596CL:0002319 neural cellMitosisUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067059287744952629194.5Browse results
SRX9940596CL:0000127 astrocyteAstrocytesUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2892555503152288506703639916301826893.5Browse results
SRX9940596CL:0000617 GABAergic neuronGABAergic neuronsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2892555503152288506702863383341927016Browse results
SRX9940596CL:2000029 central nervous system neuronNeuronUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired289255550315228850670662008123524663Browse results
SRX9940596CL:4023056 vascular leptomeningeal cell (Mmus)VLMC1UBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired289255550315228850670624009133124804.5Browse results
SRX9940596CL:0000183 contractile cellPericytes/VSMCUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2892555503152288506702552299220926073.5Browse results
SRX9940596CL:0000047 neuronal stem cellB cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067030285456758128596Browse results
SRX9940596CL:0000031 neuroblastA cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067057571998894329176.5Browse results
SRX9940596CL:0011020 neural progenitor cellC cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067015283616623827990.5Browse results
SRX9940596CL:0000115 endothelial cellEndothelial cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067016686793605927897.5Browse results
SRX9940596CL:0000095 neuron associated cellOPC/OligoUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired2892555503152288506709341728547727761Browse results
SRX9940596CL:0000065 ependymal cellEpendymal cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067046580416885329392Browse results
SRX9940596CL:0000129 microglial cellMicrogliaUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000149 4-week-old stage (mouse)Postnatal day 35 and Postnatal day 29mixedhGFAP:GFPNANAMus musculusNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired28925555031522885067011629422479027559Browse results

Showing 1 to 13 of 13 entries

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