Spatio-temporal immune zonation of the human kidney

Experiment ID:ERP120466
Technology:scRNA-Seq
Description:Tissue-resident immune cells are important for organ homeostasis and defense. The epithelium may contribute to these functions directly, or via crosstalk with immune cells. We resolved the spatio-temporal immune topology of the human kidney with a scRNAseq dataset from 40,268 mature and 27,203 fetal kidney cells. Within the epithelial compartment there were zonated patterns of immune gene expression, with pelvic epithelial anti-microbial peptide expression in mature but not fetal kidneys. Tissue-resident immune cells were evident in both fetal and mature kidney, with post-natal acquisition of infection-defense capabilities. Epithelial-immune signalling orchestrated localization of macrophages and neutrophils to regions of the kidney susceptible to infection.
DOI:10.1126/science.aat5031
Source:ERP120466 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 sapiens

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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
ERX3984855CL:0000499 stromal cellProliferating stroma progenitorUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684301619325464125578Browse results
ERX3984855CL:2000042 embryonic fibroblastProliferating fibroblastUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684309962766222146Browse results
ERX3984856CL:1001036 vasa recta cellAscending vasa recta endotheliumUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1725386621167925100111826819289Browse results
ERX3984856CL:0000097 mast cellMast cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1725386621167925100107259318812.5Browse results
ERX3984856CL:0000860 classical monocyteMNP-a/classical monocyte derivedUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251007257835520900.5Browse results
ERX3984856CL:0000875 non-classical monocyteMNP-b/non-classical monocyte derivedUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251008370936121062.5Browse results
ERX3984856CL:0000451 dendritic cellMNP-c/dendritic cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251004928531620643Browse results
ERX3984856CL:0000864 tissue-resident macrophageMNP-d/Tissue macrophageUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single172538662116792510021673118012Browse results
ERX3984856CL:0000623 natural killer cellNK cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single172538662116792510036710994723404.5Browse results
ERX3984856CL:0000921 type I NK T cellNKT cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single172538662116792510016294157322187Browse results
ERX3984856CL:1001033 peritubular capillary endothelial cellPeritubular capillary endothelium 1UBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251005071522721297.5Browse results
ERX3984856CL:0000784 plasmacytoid dendritic cellPlasmacytoid dendritic cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single172538662116792510054976918400.5Browse results
ERX3984856CL:1000507 kidney tubule cellDistinct proximal tubule 2UBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1725386621167925100130317919396.5Browse results
ERX3984856CL:0000236 B cellB cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1725386621167925100831534112624134.5Browse results
ERX3984856CL:1001106 kidney loop of Henle thick ascending limb epithelial cellThick ascending limb of Loop of HenleUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251003896819520532.5Browse results
ERX3984856CL:0005011 renal alpha-intercalated cellType A intercalated cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single172538662116792510094647718894Browse results
ERX3984856CL:0000624 CD4-positive, alpha-beta T cellCD4 T cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251001768258185525282.5Browse results
ERX3984856CL:0000625 CD8-positive, alpha-beta T cellCD8 T cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single172538662116792510056776399023923.5Browse results
ERX3984856CL:1000768 kidney connecting tubule epithelial cellConnecting tubuleUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17253866211679251004076727420762Browse results
ERX3984856CL:0002188 glomerular endothelial cellGlomerular endotheliumUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000166 72-year-old stage (human)72 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1725386621167925100111387819211Browse results

Showing 21 to 40 of 408 entries

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