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

Experiment ID:SRP303343
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 nucleus sequencing dataset of four microdissected regions of adult CD1 wild type mouse ventricular-subventricular zones (V-SVZ). Four samples (anterior-ventral, AV; anterior dorsal, AD; posterior ventral, PV; posterior dorsal, PD) were generated at the same time from the same mice, and each sample was run on its own lane of a 10x Chromium Single Cell Controller chip for single nucleus barcoding. Results: Here we present single nucleus and single whole cell 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 nucleus profiles of regionally micro-dissected ventricular-subventricular zones of 17 postnatal day 35 male (8 mice) and female (9 mice) CD1 wild type mice.
DOI:10.7554/eLife.67436
Source:SRP303343 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
SRX9940562CL:0000099 interneuronIN, Interneuron1UBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35010569620561360701537433733126560.5Browse results
SRX9940562CL:0000065 ependymal cellEpendymal, EpendymalUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35010569620561360701060994714326535.5Browse results
SRX9940562CL:0002319 neural cellMitosis, Dividing/C cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070178908432924324.5Browse results
SRX9940562CL:0000031 neuroblastA cells, A cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070773604645525934.5Browse results
SRX9940562CL:4030048 striosomal D1 medium spiny neuronSN-D1, Tac1 SN-D1UBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070942988643725938Browse results
SRX9940562CL:4023029 indirect pathway medium spiny neuronSN-D2, SN-D2UBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35010569620561360706668511931527941.5Browse results
SRX9940562CL:0000129 microglial cellMicroglia, MicrogliaUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070249921490424750.5Browse results
SRX9940562CL:0000183 contractile cellPericyte/VSMC, Pericyte/VSMCUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired350105696205613607065714262022788.5Browse results
SRX9940562CL:0000128 oligodendrocyteOligo, OligodendrocyteUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070297555510724856.5Browse results
SRX9940562CL:4023026 direct pathway medium spiny neuronSN-D1, SN-D1UBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35010569620561360706539318927027906Browse results
SRX9940562CL:0000115 endothelial cellEndothelial, EndothelialUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070213890433624684.5Browse results
SRX9940562CL:0000108 cholinergic neuronIN, CHAT NeuronUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070377998537124843Browse results
SRX9940562CL:4023051 vascular leptomeningeal cellMeningeal, Vasc LeptomeningealUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired350105696205613607023852148921264Browse results
SRX9940562CL:0000679 glutamatergic neuronEN, VGLUT1 NeuronUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070278945470824530.5Browse results
SRX9940562CL:0000047 neuronal stem cellB cells, B cellsUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070253890462324878.5Browse results
SRX9940562CL:0000095 neuron associated cellOPC/Oligo, OPC/OligodendrocyteUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070406700531825275Browse results
SRX9940562CL:0000127 astrocyteAstrocytes, AstrocytesUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3501056962056136070295710468824877Browse results
SRX9940563CL:0000679 glutamatergic neuronEN, VGLUT2 NeuronUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired2750731591581345080269236618764.5Browse results
SRX9940563CL:0000108 cholinergic neuronIN, CHAT NeuronUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired2750731591581345080445655483125123Browse results
SRX9940563CL:0000115 endothelial cellEndothelial, EndothelialUBERON:0004922 postnatal subventricular zoneVentricular-subventricular zone (brain)MmusDv:0000150 5-week-old stage (mouse)Postnatal day 35mixedCD-1NANAMus musculusNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired2750731591581345080716911578625915Browse results

Showing 1 to 20 of 67 entries

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