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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

JGAD000997

Type of data
NGS (Exome)
NGS (RNA-seq)
NGS (scRNA-seq)
NGS (Visium Spatial Gene Expression), Histological image
Xenium In Situ Gene Expression
Access criteria
Controlled-access (Type I)
Total data volume
1.0 TB
File formats
  • FASTQ
  • BAM
  • TSV
  • PARQUET
  • MTX
  • HDF5
  • TIFF
Research
hum0550
Date published
2025-11-14
Date modified
2025-11-14
DDBJ Search
JGAD000997 (opens in a new tab)
JGA Study
JGAS000855 (opens in a new tab)

Analysis method

WES

Materials and participants
renal cancer (ICD10: C64): 54 cases
tumor tissues: 125 samples
non-tumor tissues (cyst): 36 samples
  • Health status
    Affected
  • Subject count
    54 (Individual)
Disease
renal cancer (C64)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues
  • Tissue
    Cyst
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
Twist Library Preparation Kit
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh38
Mapping
BWA-MEM
Mapping quality
MAPQ > 20
Coverage (depth)
127x
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
renal cancer (ICD10: C64): 91 cases
tumor tissues: 91 samples
  • Health status
    Affected
  • Subject count
    91 (Individual)
Disease
renal cancer (C64)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
NEBNext Ultra Directional RNA Library Prep Kit for Illumina
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)

scRNA-seq

Materials and participants
renal cancer (ICD10: C64): 18 cases
tumor tissues: 24 samples
  • Health status
    Affected
  • Subject count
    18 (Individual)
Disease
renal cancer (C64)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 3' v3.1
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
read1: 28 bp
read2: 90 bp
Data use policy
NBDC data sharing policy (JGAP000001)

Xenium 空間トランスクリプトーム

Materials and participants
renal cancer (ICD10: C64): 3 cases
tumor tissues: 4 samples
  • Health status
    Affected
  • Subject count
    3 (Individual)
Disease
renal cancer (C64)
Sample description
tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Spatial transcriptomics
Target
N/A
Reagent kit
Xenium Human Multi-Tissue and Cancer Panel
Xenium In Situ Gene Expression
Platform
10x Genomics Xenium Analyzer
Analysis method
Xenium Analyzer
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): 16 cases
tumor tissues: 22 samples
  • Health status
    Affected
  • Subject count
    16 (Individual)
Disease
renal cancer (C64)
Sample description
tumor 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 Spatial Gene Expression
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
read1: 28 bp
read2: 50 bp
Reference genome
GRCh38
Analysis method
Space Ranger Pipeline (version 1.3.1)
Data use policy
NBDC data sharing policy (JGAP000001)