Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000871

Type of data
NGS (scRNA-seq)
NGS (Visium Spatial Gene Expression), Histological image
Access criteria
Controlled-access (Type I)
Total data volume
806 GB
File formats
  • FASTQ
  • TSV
  • CSV
  • JSON
  • MTX
  • HDF5
  • PNG
  • GZIP
Research
hum0476
Date published
2025-01-08
Date modified
2025-06-11
DDBJ Search
JGAD000871 (opens in a new tab)
JGA Study
JGAS000736 (opens in a new tab)

Analysis method

scRNA-seq

Materials and participants
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
  • Health status
    Affected
  • Subject count
    14 (Individual)
Disease
renal cancer (C64, N028, N088, N26, E142, N12)
Sample description
RNAs extracted from non-tumor tissues
  • Tissue
    Kidney
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 3' v3.1
Fragmentation
10x Genomics's protocol
Platform
Illumina NextSeq 2000
Read type
Paired-end
Read length
Read 1: 28 bp
Read2: 90 bp
Reference genome
GRCh38
Mapping
STAR
QC and filtering
N/A
Analysis method
Cell Ranger 4.0.0
Gene count
53 (SC)
28,183 (Total genes detected)
2046 (Median genes per cell)
68 (SC)
28,837 (Total genes detected)
2665 (Median genes per cell)
136 (SC)
28,357 (Total genes detected)
2263 (Median genes per cell)
176 (SC)
29,154 (Total genes detected)
2588 (Median genes per cell)
204 (SC)
29,034 (Total genes detected)
2848 (Median genes per cell)
286 (SC)
28,351 (Total genes detected)
2680 (Median genes per cell)
Processed data type
Gene expression matrix
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)

Visium 空間トランスクリプトーム + 病理画像

Materials and participants
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
  • Health status
    Affected
  • Subject count
    32 (Individual)
Disease
renal cancer (C64, N028, N088, N26, E142, N12)
Sample description
non-tumor samples from surgically resected tissues
  • Tissue
    Kidney
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Histological image
Spatial transcriptomics
Target
N/A
Sample processing
Histological staining: hematoxylin-eosin staining
Reagent kit
Visium Human Transcriptome Probe Kit
Visium Spatial Gene Expression for FFPE
Fragmentation
N/A
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
Read 1: 28 bp
Read2: 50 bp
Reference genome
GRCh38
Analysis method
Space ranger, Seurat, Loupe
Processed data type
Histological image
Spatial gene expression data
Data use policy
NBDC data sharing policy (JGAP000001)