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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

JGAD000682

Type of data
NGS (Exome, RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
5.6 TB
File formats
  • FASTQ
  • BAM
  • BAI
  • CEL
  • CSV
Research
hum0030
Date published
2024-05-13
Date modified
2024-07-09
DDBJ Search
JGAD000682 (opens in a new tab)
JGA Study
JGAS000560 (opens in a new tab)

Analysis method

WES

Materials and participants
High-grade serous ovarian carcinoma (ICD10: C56.12): 78 cases
(tumor tissue: 82 samples, non-tumor tissue: 78 samples)
Ovarian clear cell adenocarcinoma (ICD10: C56.14): 78 cases
(tumor tissue: 78 samples, non-tumor tissue: 78 samples)
  • Health status
    Affected
  • Subject count
    156 (Individual)
Disease
High-grade serous ovarian carcinoma (C56)
Ovarian clear cell adenocarcinoma (C56)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues (peripheral blood cells)
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon V4
SureSelect Human All Exon V5
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina HiSeq 2000
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh37
Mapping
BWA, Novoalign
Mapping quality
MAPQ>20
Coverage (depth)
tumor: 115.6x
normal: 108.4x
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
High-grade serous ovarian carcinoma (ICD10: C56.12): 77 cases
(tumor tissue: 77 samples)
  • Health status
    Affected
  • Subject count
    77 (Individual)
Disease
High-grade serous ovarian carcinoma (C56)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq Stranded mRNA Library Prep Kit
Fragmentation
Including library prep kit protocol
Platform
Illumina HiSeq 2000
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh37
Mapping
STAR (V.2.5.2a)
Mapping quality
MAPQ>20
QC and filtering
N/A
Analysis method
Cufflinks (v2.1.1)
Gene count
38,515 genes
Processed data type
FPKM
Data use policy
NBDC data sharing policy (JGAP000001)

メチル化アレイ

Materials and participants
High-grade serous ovarian carcinoma (ICD10: C56.12): 97 cases
(tumor tissue: 92 samples, non-tumor tissue: 5 samples)
Ovarian clear cell adenocarcinoma (ICD10: C56.14): 85 cases
(tumor tissue: 82 samples, non-tumor tissue: 3 samples)
  • Health status
    Affected
  • Subject count
    182 (Individual)
Disease
High-grade serous ovarian carcinoma (C56)
Ovarian clear cell adenocarcinoma (C56)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues (peripheral blood cells)
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Methylation array
Target
N/A
Reagent kit
Infinium HumanMethylation450 BeadChip Kit
Platform
Illumina Infinium HumanMethylation450
QC and filtering
N/A
Normalization
Following the standard protocol of Genome Studio
Analysis method
Genome Studio
Probe count
485,577
Data use policy
NBDC data sharing policy (JGAP000001)

発現アレイ

Materials and participants
Ovarian clear cell adenocarcinoma (ICD10: C56.14): 89 cases
(tumor tissue: 89 samples)
  • Health status
    Affected
  • Subject count
    89 (Individual)
Disease
Ovarian clear cell adenocarcinoma (C56)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Expression array
Target
N/A
Reagent kit
GeneChip 3' IVT Express Kit
Platform
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
QC and filtering
N/A
Analysis method
GeneChip® Operating Software (GCOS, Affymetrix)
Data use policy
NBDC data sharing policy (JGAP000001)