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
Download:
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

List of assays

Show

entries

Showing 1 to 20 of 408 entries

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:0000134 mesenchymal stem cellStroma progenitorUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684307520878682727291Browse results
ERX3984855CL:0002371 somatic cellDistal renal vesicleUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684301330753439725858.5Browse results
ERX3984855CL:0008019 mesenchymal cellCap mesenchymeUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684303918905577826885Browse results
ERX3984855CL:0000236 B cellProliferating B cellUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single332104638209616843034203818231.5Browse results
ERX3984855CL:0000653 glomerular visceral epithelial cellPodocyteUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3321046382096168430329875273623930.5Browse results
ERX3984855CL:0000066 epithelial cellPelvic epithelium - distal UBUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3321046382096168430724983297324322Browse results
ERX3984855CL:0000623 natural killer cellNK cellUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3321046382096168430790310618664.5Browse results
ERX3984855CL:0000540 neuronNeuronUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684304451847720974.5Browse results
ERX3984855CL:0000186 myofibroblast cellMyofibroblast 1UBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3321046382096168430344801155723705Browse results
ERX3984855CL:0000576 monocyteMonocyteUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single332104638209616843026884318052Browse results
ERX3984855CL:0000556 megakaryocyteMegakaryocyteUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684304587929920171Browse results
ERX3984855CL:0000235 macrophageMacrophage 2UBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single332104638209616843069127518526Browse results
ERX3984855CL:1000909 kidney loop of Henle epithelial cellLoop of HenleUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684309569862822223Browse results
ERX3984855CL:0001065 innate lymphoid cellInnate like lymphocyteUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single332104638209616843050327418407.5Browse results
ERX3984855CL:0000057 fibroblastFibroblast 1UBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3321046382096168430954645305725049Browse results
ERX3984855CL:0000764 erythroid lineage cellErythroidUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single332104638209616843013603029920222Browse results
ERX3984855CL:0000115 endothelial cellEndotheliumUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684301605650431925597Browse results
ERX3984855CL:0002306 epithelial cell of proximal tubuleProximal tubuleUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3321046382096168430343909156724021Browse results
ERX3984855CL:0005009 renal principal cellCNT/PC - proximal UBUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684301996400601026056.5Browse results
ERX3984855CL:0000624 CD4-positive, alpha-beta T cellCD4 T cellUBERON:0000081 metanephrosFetal Kidney flow sorted CD45-HsapDv:0000051 14th week post-fertilization stage (human)13.85 weeksfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single33210463820961684301097312218874.5Browse results

Showing 1 to 20 of 408 entries

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again