scRNA sequencing analysis for human ureters and patient derived ureter oragnoid

Experiment ID:SRP337049
Technology:scRNA-Seq
Description:Tissue engineering offers a promising treatment strategy for ureteral strictures. Successful ureter engineering is necessitated by detailed understanding of the tissue architecture, cellular heterogeneity, and signaling pathways underlying regeneration. We define and spatially map cell populations within the human ureter by using a combinatorial approach: single-cell RNA sequencing, 10X Visium spatial transciptomics, and immunofluorescence. The stromal and urothelial cell populations are analyzed in detail, and we infer potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Specifically, we analyze and experimentally validate the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells support organoid generation in vitro, and accurately predict the differentiation trajectory of basal stem cells, to terminally differentiated umbrella cells, in vivo. Our results highlight essential processes involved in adult ureter tissue homeostasis, and provide a toolkit for guiding ureter tissue engineering. Overall design: 10 normal human ureters each were subjected to RNA sequencing at single cell resolution on Novaseq using 10X Gemonics library preparation platform. Data was processed using Cellranger 4.0.0 and anayzed using Seurat v3.2.1 to characterize various cell types and understand finer details of the regenrative pathways in the ureter urothelium. This was further explored by analyzing single cell RNA sequencing data from human ureter derived organoid (generated in the same manner as the 10 ureter samples). Freshly processed and thawed tissue sample from the same human subject was used as control to further understand the urothelial regenerative pathways.
DOI:10.1016/j.devcel.2022.07.004
Source:SRP337049 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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Showing 1 to 20 of 117 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
SRX12187862CL:1000486 basal cell of urothelium0_Basal cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired493982706270511316018198684615027579.5Browse results
SRX12187862CL:0000115 endothelial cell11_Endothelial cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired49398270627051131601174794164324904Browse results
SRX12187862CL:1000706 ureter urothelial cell14_UrothelialUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired493982706270511316040706384323698Browse results
SRX12187862CL:0000623 natural killer cell10_NK cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired493982706270511316023723955423051Browse results
SRX12187862CL:0000057 fibroblast19_FibroblastsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired49398270627051131607655533421709.5Browse results
SRX12187862CL:0000097 mast cell17_Mast cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired49398270627051131609090727321193.5Browse results
SRX12187862CL:0000236 B cell12_B cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired493982706270511316030235361723027Browse results
SRX12187862CL:0000738 leukocyte16_LeucocytesUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired493982706270511316032297267722772.5Browse results
SRX12187862CL:0000084 T cell3_T cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired49398270627051131601008248112124561Browse results
SRX12187862CL:1000979 ureter smooth muscle cell13_Smooth Muscle cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired49398270627051131601200932121324714Browse results
SRX12187862CL:0000910 cytotoxic T cell2_Cytotoxic T cellsUBERON:0000056 ureterhuman ureterHsapDv:0000169 75-year-old stage (human)75femaleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired493982706270511316087209298124576Browse results
SRX12187863CL:1000706 ureter urothelial cell14_UrothelialUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55877525414678961502923954287625582Browse results
SRX12187863CL:0000738 leukocyte16_LeucocytesUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55877525414678961503825918820299.5Browse results
SRX12187863CL:1000979 ureter smooth muscle cell13_Smooth Muscle cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired558775254146789615054478886524248.5Browse results
SRX12187863CL:0000910 cytotoxic T cell2_Cytotoxic T cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired558775254146789615014226442222377.5Browse results
SRX12187863CL:0000097 mast cell17_Mast cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired558775254146789615096038018742Browse results
SRX12187863CL:0000236 B cell12_B cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55877525414678961502049413919659.5Browse results
SRX12187863CL:0000084 T cell3_T cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired558775254146789615013369237622017Browse results
SRX12187863CL:0000623 natural killer cell10_NK cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired55877525414678961503037115420397Browse results
SRX12187863CL:1000486 basal cell of urothelium0_Basal cellsUBERON:0000056 ureterhuman ureterHsapDv:0000163 69-year-old stage (human)69maleNANANAHomo sapiensNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired558775254146789615015536310504627354.5Browse results

Showing 1 to 20 of 117 entries

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