NBDC Research ID: hum0476.v1
SUMMARY
Aims: To establish a foundation for understanding the functions of kidney component cells and the biology of renal disease. Single cell and spatial transcriptome analyses of human kidney component cells will be performed to analyze the gene expression profiles of those cells and explore their relationship between the gene expression profiles and clinical parameters. The research foundation established here is worthwhile for understanding disease mechanisms in the kidney or discovering novel therapeutic drugs for renal disease.
Methods: Single cell RNA sequencing analysis, Spatial transcriptome analysis (Visium)
Participants/Materials: Noncancerous tissue (including other findings) from surgically removed from 32 renal cancer patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000736 | Controlled-access (Type I) | 2025/01/07 |
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MOLECULAR DATA
| Participants/Materials |
renal cancer (ICD10: C64, N028, N088, N26, E142, N12): 32 cases normal tissue: 3 samples findings of IgA nephropathy: 3 samples findings of early diabetic changes: 2 samples findings of IgA deposition: 2 samples findings of glomerular hyperplasia: 1 sample findings of nephrosclerosis and diabetic nephropathy: 1 sample findings of nephrosclerosis and IgA deposition: 1 sample findings of diabetic nephropathy: 1 sample |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 2000] |
| Library Source | RNAs extracted from non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Automated Single Cell 3' Reagent Kits v3.1 |
| Fragmentation Methods | 10x Genomics's protocol |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | Read 1: 28bp, Read2: 90bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000871 |
| Total Data Volume | 806.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
renal cancer (ICD10: C64, N028, N088, N26, E142, N12): 32 cases normal tissue: 9 samples findings of IgA nephropathy: 6 samples findings of early diabetic changes: 2 samples findings of IgA deposition: 2 samples findings of glomerular hyperplasia: 1 sample findings of nephrosclerosis: 7 samples findings of nephrosclerosis and diabetic nephropathy: 1 sample findings of nephrosclerosis and IgA deposition: 2 samples findings of diabetic nephropathy: 1 sample findings of tubulointerstitial nephritis: 1 sample |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | non-tumor samples from surgically resected tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial for FFPE Gene Expression Kit, Visium Human Transcriptome Probe Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | Read1: 28bp Read2: 50bp |
| Software | Space ranger, Seurat, Loupe |
| Reference | refdata-gex-GRCh38-2020-A, Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000871 |
| Total Data Volume | 806.0 GB (fastq, h5, json, png) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shokichi Naito
Affiliation: Nephrology, Kitasato University school of Medicine
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Inflammatory molecules in the glomerular endothelium in mild IgA-Nephropathy identified by single-cell and spatial transcriptome | doi:10.1101/2024.10.30.621002 | JGAD000871 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
