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
ERX3984857CL:0000576 monocyteProliferating monocyteUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000050 13th week post-fertilization stage (human)12 weeksmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single377032222238562070035775318168.5Browse results
ERX3984857CL:2000042 embryonic fibroblastProliferating fibroblastUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000050 13th week post-fertilization stage (human)12 weeksmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single37703222223856207008807246521881Browse results
ERX3984858CL:0000236 B cellB cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647022279952222531.5Browse results
ERX3984858CL:0000623 natural killer cellNK cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464705465626921077.5Browse results
ERX3984858CL:0000921 type I NK T cellNKT cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464703312921820167Browse results
ERX3984858CL:1001033 peritubular capillary endothelial cellPeritubular capillary endothelium 1UBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464701217810419358.5Browse results
ERX3984858CL:1000507 kidney tubule cellProximal tubuleUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647077883298323429.5Browse results
ERX3984858CL:1001106 kidney loop of Henle thick ascending limb epithelial cellThick ascending limb of Loop of HenleUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647023632718108Browse results
ERX3984858CL:0005011 renal alpha-intercalated cellType A intercalated cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647013057263021853Browse results
ERX3984858CL:0000624 CD4-positive, alpha-beta T cellCD4 T cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464703040721220098Browse results
ERX3984858CL:0000625 CD8-positive, alpha-beta T cellCD8 T cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464705866529321105Browse results
ERX3984858CL:0002188 glomerular endothelial cellGlomerular endotheliumUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464701199510119314Browse results
ERX3984858CL:0005010 renal intercalated cellIntercalated cell (indistinct)UBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647071576118736Browse results
ERX3984858CL:0000097 mast cellMast cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647039424618233.5Browse results
ERX3984858CL:0000860 classical monocyteMNP-a/classical monocyte derivedUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464702404218319574Browse results
ERX3984858CL:0000451 dendritic cellMNP-c/dendritic cellUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single244914471643464702053117019545Browse results
ERX3984858CL:0000864 tissue-resident macrophageMNP-d/Tissue macrophageUBERON:0000082 adult mammalian kidneyKidney biopsy sample - CortexHsapDv:0000147 53-year-old stage (human)53 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single2449144716434647044265318377Browse results
ERX3984859CL:0000134 mesenchymal stem cellStroma progenitorUBERON:0000081 metanephrosFetal kidney flow sorted CD45+HsapDv:0000054 17th week post-fertilization stage (human)16 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3477696642065601920251685150523576.5Browse results
ERX3984859CL:1000698 kidney resident macrophageProliferating macrophageUBERON:0000081 metanephrosFetal kidney flow sorted CD45+HsapDv:0000054 17th week post-fertilization stage (human)16 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3477696642065601920704511333424458Browse results
ERX3984859CL:0002371 somatic cellDistal renal vesicleUBERON:0000081 metanephrosFetal kidney flow sorted CD45+HsapDv:0000054 17th week post-fertilization stage (human)16 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single34776966420656019201312415619338.5Browse results

Showing 61 to 80 of 408 entries

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