Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons

Experiment ID:SRP167086
Technology:scRNA-Seq
Description:Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.
DOI:10.1038/s41467-021-25444-3
Source:SRP167086 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
SRX4947724CL:0011028 olfactory ensheathing cellOEC1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5670786683605577020527817120724740.5Browse results
SRX4947724CL:0000129 microglial cellMicroG1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired567078668360557702023103973123755.5Browse results
SRX4947724CL:0000540 neuronN1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5670786683605577020943640161425372Browse results
SRX4947724CL:0008019 mesenchymal cellMes1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired567078668360557702027100376724177.5Browse results
SRX4947724CL:0000127 astrocyteAstro1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired56707866836055770201027785159225449.5Browse results
SRX4947724CL:0000071 blood vessel endothelial cellEC1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5670786683605577020864072146625147.5Browse results
SRX4947724CL:0000235 macrophageMφUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired567078668360557702015179061923488.5Browse results
SRX4947724CL:0002453 oligodendrocyte precursor cellOPCUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5670786683605577020221023102224119Browse results
SRX4947724CL:0000576 monocyteMonoUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired567078668360557702015983262823430Browse results
SRX4947724CL:0008034 mural cellMural1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired567078668360557702013192368923434.5Browse results
SRX4947724CL:0000232 erythrocyteRBCsUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired56707866836055770207038310220083Browse results
SRX4947724CL:0000128 oligodendrocyteMyOligoUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5670786683605577020359070111524028.5Browse results
SRX4947725CL:0011028 olfactory ensheathing cellOEC1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5028922012880889080653103139924941.5Browse results
SRX4947725CL:0000129 microglial cellMicroG1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5028922012880889080372730103824148.5Browse results
SRX4947725CL:0000540 neuronN1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5028922012880889080982670181825438.5Browse results
SRX4947725CL:0008019 mesenchymal cellMes1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired502892201288088908016452960223615Browse results
SRX4947725CL:0000127 astrocyteAstro1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5028922012880889080826105157025278.5Browse results
SRX4947725CL:0000071 blood vessel endothelial cellEC1UBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired5028922012880889080634056134924948Browse results
SRX4947725CL:0000235 macrophageMφUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired502892201288088908014424960023322Browse results
SRX4947725CL:0002453 oligodendrocyte precursor cellOPCUBERON:0002264 olfactory bulbOlfactory bulbMmusDv:0000137 3-6 month-old mature stage (mouse)14-20 weeksmixedC57BL/6NJNANAMus musculusNA10X Genomics V2NextSeq 500THREE_PRIMECELL0paired502892201288088908018030895323901.5Browse results

Showing 1 to 20 of 48 entries

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