Transcriptomic Taxonomy and Neurogenic Trajectories of Adult Human, Macaque and Pig Hippocampal and Entorhinal Cells

Experiment ID:SRP343046
Technology:scRNA-Seq
Description:The hippocampal-entorhinal system supports cognitive functions, has lifelong neurogenic capabilities in many species, and is selectively vulnerable to Alzheimer's disease. To investigate neurogenic potential and cellular diversity, we profiled single-nucleus transcriptomes in five hippocampal-entorhinal subregions in human, macaque, and pig. Integrated cross-species analysis revealed robust transcriptomic and histologic signatures of neurogenesis in adult mouse, pig and macaque, but not humans. Doublecortin (DCX), a widely accepted marker of newly generated granule cells, was detected in diverse human neurons, but it did not define immature neuron populations. To explore species differences in cellular diversity and implications for disease, we characterized subregion-specific transcriptomically-defined cell types and transitional changes from the three-layered archicortex to the six-layered neocortex. Notably, METTL7B defined subregion-specific excitatory neurons and astrocytes in primates, associated with endoplasmic reticulum and lipid droplet proteins, including Alzheimer's disease-related proteins. Together this resource reveals cell-type- and species-specific properties shaping hippocampal-entorhinal neurogenesis and function. Overall design: snRNA-seq of hippocampal-entorhinal system in 6 human donors, dentate gyrus in 3 rhesus macaque donors, and adult hippocampus in 9 pig donors with different postmortem intervals (30 minutes, 1 hour, 7 hour)
DOI:10.1016/j.neuron.2021.10.036
Source:SRP343046 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiensscRNA-Seq droplet-based processed expression values per cell population in Macaca mulattascRNA-Seq droplet-based H5AD data per cell in Macaca mulattascRNA-Seq droplet-based processed expression values per cell population in Sus scrofascRNA-Seq droplet-based H5AD data per cell in Sus scrofa

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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
SRX12770671CL:0002319 neural cellCA1 SubUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired4169134991874430410207492701165720950.5Browse results
SRX12770671CL:4023072 brain vascular cellvascular cellUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired4169134991874430410819391627119293.5Browse results
SRX12770671CL:0000540 neuroninhibitory neuronUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired41691349918744304107792359987220560Browse results
SRX12770671CL:0000128 oligodendrocyteoligodendrocyteUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired416913499187443041016356466902520803.5Browse results
SRX12770671CL:0000738 leukocyteimmuneUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired41691349918744304102305186636419798Browse results
SRX12770671CL:0002604 astrocyte of the hippocampusastrocyteUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired41691349918744304102085651695819847Browse results
SRX12770671CL:0000031 neuroblastneuroblastUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired41691349918744304101440508648519565Browse results
SRX12770671CL:0001033 hippocampal granule cellgranule cellUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired4169134991874430410107548921007920658Browse results
SRX12770671CL:0002453 oligodendrocyte precursor celloligodendrocyte precursor cellUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired41691349918744304101954514674519746Browse results
SRX12770672CL:0002319 neural cellCA1 SubUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3574009331776781230215870631166421018.5Browse results
SRX12770672CL:4023072 brain vascular cellvascular cellUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812301074993633919534Browse results
SRX12770672CL:0000540 neuroninhibitory neuronUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired3574009331776781230108694011027920789.5Browse results
SRX12770672CL:0000128 oligodendrocyteoligodendrocyteUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812307778918764920423.5Browse results
SRX12770672CL:0000738 leukocyteimmuneUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812301587048570219467.5Browse results
SRX12770672CL:0002604 astrocyte of the hippocampusastrocyteUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812302191553652219868.5Browse results
SRX12770672CL:0000031 neuroblastneuroblastUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812301142637606519349Browse results
SRX12770672CL:0001033 hippocampal granule cellgranule cellUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812307614498936920493.5Browse results
SRX12770672CL:0002453 oligodendrocyte precursor celloligodendrocyte precursor cellUBERON:0001954 Ammon's hornHippocampusSscrDv:0000045 13-week-old stage (pig)0.25YfemaleNANANASus scrofaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired35740093317767812301152404587219322Browse results
SRX12770679CL:0000120 granule cellgranule cellUBERON:0001885 dentate gyrus of hippocampal formationDentate gyrusMmulDv:0000029 9-year-old stage (macaque)9.89YfemaleNANANAMacaca mulattaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired13628277648799114012631592755320557Browse results
SRX12770679CL:4023072 brain vascular cellvascular cellUBERON:0001885 dentate gyrus of hippocampal formationDentate gyrusMmulDv:0000029 9-year-old stage (macaque)9.89YfemaleNANANAMacaca mulattaNA10X Genomics V3Illumina HiSeq 4000THREE_PRIMENUCLEUS0paired13628277648799114045464224915247.5Browse results

Showing 1 to 20 of 610 entries

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