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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

JGAD000858

Type of data
NGS (Exome)
NGS (RNA-seq)
NGS (WGS)
NGS (scRNA-seq)
NGS (Visium Spatial Gene Expression), Histological image
Access criteria
Controlled-access (Type I)
Total data volume
5.0 TB
File formats
  • FASTQ
  • BAM
  • TSV
  • CSV
  • JSON
  • MTX
  • PNG
Research
hum0470
Date published
2025-07-09
Date modified
2025-12-11
DDBJ Search
JGAD000858 (opens in a new tab)
JGA Study
JGAS000725 (opens in a new tab)

Analysis method

WES

Materials and participants
Urothelial carcinoma (ICD10: C679): 1 case
tumor tissues: 58 samples from 8 organs
  • Health status
    Affected
  • Subject count
    58 (Sample)
Disease
Urothelial carcinoma (C679)
Sample description
DNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon V6
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
MGI DNBSEQ-G400
Read type
Paired-end
Read length
100 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
Urothelial carcinoma (ICD10: C679): 1 case
tumor tissues: 58 samples from 8 organs
  • Health status
    Affected
  • Subject count
    58 (Sample)
Disease
Urothelial carcinoma (C679)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq RNA Exome
Fragmentation
chemical fragmentation
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)

WGS

Materials and participants
Urothelial carcinoma (ICD10: C679): 1 case
tumor tissues: 8 samples from 8 organs
  • Health status
    Affected
  • Subject count
    8 (Sample)
Disease
Urothelial carcinoma (C679)
Sample description
DNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
SureSelect Human All Exon V6
SureSelect XT Reagent Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
MGI DNBSEQ-G400
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)

scRNA-seq

Materials and participants
Urothelial carcinoma (ICD10: C679): 1 case
tumor tissues: 5 samples from 5 organs
  • Health status
    Affected
  • Subject count
    5 (Sample)
Disease
Urothelial carcinoma (C679)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Fixed RNA Profiling Kit
Fragmentation
included in the above protocol
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
118 bp
Reference genome
GRCh38
Mapping
Cell Ranger v9.0.0
Mapping quality
Reads mapped to probe set: 97.2%
Reads confidently mapped to probe set: 96.2%
Reads confidently mapped to filtered probe set: 93.8%
Reads half-mapped to probe set: 0.5%
Reads split-mapped to probe set: 0.5%
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
Urothelial carcinoma (ICD10: C679): 1 case
tumor tissues: 7 samples from 5 organs
  • Health status
    Affected
  • Subject count
    7 (Sample)
Disease
Urothelial carcinoma (C679)
Sample description
tumor samples from surgically resected tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Histological image
Spatial transcriptomics
Target
N/A
Sample processing
Histological staining: hematoxylin-eosin staining
Reagent kit
Visium CytAssist Spatial Gene Expression for FFPE
Visium Human Transcriptome Probe Kit
Visium Spatial Gene Expression for FFPE
Fragmentation
N/A
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
78 bp
Reference genome
GRCh38
Analysis method
Space Ranger v1.3.1, v3.1.2
Data use policy
NBDC data sharing policy (JGAP000001)