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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

JGAD000663

Type of data
NGS (WGS, Exome, RNA-seq)
Digital multiplexed gene expression analysis
Access criteria
Controlled-access (Type I)
Total data volume
1.1 TB
File formats
  • BAM
  • TXT
Research
hum0355
Date published
2023-06-21
Date modified
2023-06-21
DDBJ Search
JGAD000663 (opens in a new tab)
JGA Study
JGAS000544 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
LBL-C0269-03_nCounter-Human-Immunology-V2-Panel-Gene-List.xlsx205 KB

Analysis method

WGS

Materials and participants
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 1 case
peripheral blood: 1 sample (for germline VHL gene alteration testing)
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
VHL (Q858)
hereditary ccRCC (C64)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
bwa
Mapping quality
10x coverage width: 99%
Coverage (depth)
34x
Data use policy
NBDC data sharing policy (JGAP000001)

WES

Materials and participants
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 10 cases (98 samples)
primary tumor: 10 cases (81 samples)
metastatic tumor: 1 case (7 samples [1 lung, 3pleura, and 3 lymph nodes])
peripheral blood: 10 cases (10 samples)
  • Health status
    Affected
  • Subject count
    10 (Individual)
Disease
VHL (Q858)
hereditary ccRCC (C64)
Sample description
DNAs extracted from tumor tissues and peripheral blood cells
  • Tissue
    Lung, Lymph node, Peripheral blood, Pleura
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon V6
SureSelect XT HS
SureSelect XT Reagent Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina NextSeq 500
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
bwa
Mapping quality
Median 30x coverage width: 97%
Coverage (depth)
166x
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 7 cases (49 samples)
primary tumor: 7 cases (49 samples)
  • Health status
    Affected
  • Subject count
    7 (Individual)
Disease
VHL (Q858)
hereditary ccRCC (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 II RNA Library Prep Kit for Illumina
Fragmentation
Heat treatment
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
bwa
Mapping quality
Median mapped reads 9,639,928
Gene count
26,718
Data use policy
NBDC data sharing policy (JGAP000001)

Direct Digital Count (nCounter)

Materials and participants
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 9 cases (82 samples)
primary tumor: 9 cases (76 samples)
normal renal cortex: 6 cases (6 samples)
  • Health status
    Affected
  • Subject count
    9 (Individual)
Disease
VHL (Q858)
hereditary ccRCC (C64)
Sample description
RNAs extracted from tumor and non-tumor tissues
  • Tissue
    Renal cortex
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
nCounter (NanoString)
Target
594 genes
Reagent kit
nCounter Human Immunology V2 Panel CodeSet
Platform
NanoString Technologies nCounter Digital Analyzer
QC and filtering
nSolver analysis software v4.0.70
Analysis method
nSolver analysis software v4.0.70
Data use policy
NBDC data sharing policy (JGAP000001)