hum0030 Release Note

Research ID	Release Date	Type of Data
hum0030.v5	2026/04/22	NGS (Target bisulfite-seq)
hum0030.v4	2025/07/01	NGS (Exome)
hum0030.v3	2024/07/05	Methylation array, Expression array
hum0030.v2	2024/05/10	NGS (Exome, RNA-seq)
hum0030.v1	2015/04/21	CNV analysis using 57 ovarian carcinoma patients

 

hum0030.v5

DNAs extracted from tumor tissues of 86 endometrial cancer patients were used for the HLA-A region targeted bisulfite sequencing analysis. Fastq files are provided.

 

hum0030.v4

DNAs extracted from tumor and non-tumor tissues of 189 ovarian cancer patients were used for the whole exome sequencing analyses. Fastq and bam files are provided.

 

hum0030.v3

DNAs/RNAs extracted from tumor and non-tumor tissues of high-grade serous ovarian carcinoma or ovarian clear cell adenocarcinoma patients were used for the methylation array and expression array analyses. Txt and CEL files are provided.

 

hum0030.v2

DNAs/RNAs extracted from tumor and non-tumor tissues of high-grade serous ovarian carcinoma or ovarian clear cell adenocarcinoma patients were used for the whole exome sequencing and RNA sequencing analyses. Fastq, bam, and csv files are provided.

 

hum0030.v1

Signal intensities for 260K CNVs of 57 ovarian carcinomas were decided by using of GeneChip Human Mapping 250K Nsp Arrays (Affymetrix) (CEL files).

 

Note:

hum0201 Release Note

Research ID	Release Date	Type of Data
hum0201.v9	2026/04/21	NGS (Exome, RNA-seq)
hum0201.v8	2024/08/28	NGS (Exome, RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq)
hum0201.v7	2022/12/27	Processed data of JGAD000335 by JGA
hum0201.v6	2022/08/05	NGS (scRNA-seq, RNA-seq, Exome)
hum0201.v5	2022/06/06	NGS (RNA-seq)
hum0201.v4	2021/11/19	NGS (RNA-seq, ChIP-seq)
hum0201.v3	2020/11/20	NGS (RNA-seq)
hum0201.v2	2020/10/06	NGS (WGS, RNA-seq)
hum0201.v1	2019/12/20	NGS (Exome)

 

hum0201.v9

DNAs/RNAs extracted from organoids established from normal and tumor tissues of the patients with colon cancer, duodenal adenoma and stomach cancer or a healthy individual or genetically engineered organoids were used for the whole exome and RNA sequencing analyses. Fastq files are provided.

 

hum0201.v8

DNAs/RNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids were used for the whole exome, RNA, scRNA, ATAC and ChIP sequencing analyses. Fastq and bed files are provided.

 

hum0201.v7

The alignment results [CRAM], variant call results per sample [gVCF], and variant call results per dataset [aggregated VCF] processed JGAD000335 in a certain workflow were provided. If you plan to use the data, please indicate both original data (JGAD000335) and processed data (JGAD000687) on the application form for data use.

 

hum0201.v6

RNAs extracted from normal colonic tissue from a neoplastic disease patient was used for the single cell RNA sequencing analysis. DNAs and RNAs extracted from organoids established from healthy normal colonic tissues of the patients were used for the whole genome and RNA sequencing analyses. Fastq files are provided.

 

hum0201.v5

RNAs extracted from organoids derived from colon cancer tissues from neoplastic disease patients were used for the RNA sequencing analysis. Fastq files are provided.

 

hum0201.v4

DNAs and RNAs extracted from organoids established from colon cancer tissues and a normal epithelial tissue of the patients were used for RNA sequencing and ChIP-seq analyses. Fastq files are provided.

 

hum0201.v3

Gene expression of 2D normal duodenum organoids with or without medium rotation was analyzed. Total RNA was extracted from organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation, and sequenced with HiSeq X Ten. Fastq files are provided.

 

hum0201.v2

DNAs and RNAs extracted from peripheral blood cells and organoids established from normal and cancer tissues of the patients were used for the whole genome and RNA sequencing analysis. Fastq files are provided.

 

hum0201.v1

DNAs extracted from inflammatory/tumor tissues from gastrointestinal inflammatory disease patients, peripheral blood cells from patients/controls, and the organoids established from epithelial tissues from patients were used for the whole exome sequencing analysis. Fastq files are provided.

 

Note：

NBDC Research ID: hum0201.v9

 

SUMMARY

Aims: Search for differences in genomics and traits among normal cells, digestive non-tumor cells (inflammatory cells), and tumor cells

Methods:

JGAS000199: The organoids were established from epithelial tissues from patients, and cultured. DNAs were extracted from the organoids and peripheral blood cells. Whole exome sequencing analysis was performed to identify the somatic mutations.

JGAS000237: Organoids were established from tissue samples (normal and cancer) obtained from any cancer patients. The organoids were cultured, and DNA / RNA was extracted from the organoids for whole genome / RNA sequencing analysis to identify the somatic mutations. Blood samples were substituted when normal tissue samples were not available.

JGAS000256: RNA was extracted from the 2D-cultured normal duodenal organoids with or without medium rotation. RNA sequencing was performed to identify the changes in gene expression after culture medium rotation.

JGAS000378: RNA sequencing and Chip-seq analysis for the organoids derived from colon cancer tissues and a normal epithelial tissue from patients

JGAS000350: RNA sequencing analysis for the organoids derived from colon cancer tissues

JGAS000550: single cell RNA sequencing analysis for normal colonic tissue and RNA sequencing or Whole Exome sequencing analyses for the organoids derived from healthy normal colonic tissues in the neoplastic disease patient

JGAS000719: Organoids were derived from surgically resected specimens, endoscopic ultrasound-guided fine needle aspiration samples, brushing samples, pleural effusion, and ascites of patients with pancreatic cancer. Genetically engineered human pancreatic duct organoids were made by introducing cancer gene mutations in duct organoids using CRISPR-Cas9. DNAs/RNAs were extracted from the organoids for whole exome sequencing, RNA sequencing, single cell RNA sequencing, ATAC sequencing, and ChIP sequencing analyses.

JGAS000881: Organoids were established from the tumor and normal counterpart of patients with duodenal tumor. Also, organoids were established from healthy ileum, colon or duodenum of patients with colon cancer, stomach cancer or a healthy individual and were further genetically engineered with CRISPR-Cas9. DNAs/RNAs were extracted from the organoids for whole exome sequencing and RNA sequencing analyses.

Participants/Materials:

JGAS000199: Controls who underwent colonoscopy, gastrointestinal inflammatory disease patients, and neoplastic disease patients

JGAS000237: Neoplastic disease patients

JGAS000256: Normal duodenum tissue from a neoplastic disease patient

JGAS000378: Colon cancer tissues and a normal epithelial tissue from neoplastic disease patients

JGAS000350: Neoplastic disease patient

JGAS000550: Neoplastic disease patient

JGAS000719: Pancreatic cancer patients

JGAS000881: Colon cancer patients, duodenal adenoma patients, a stomach cancer patient and a healthy individual

 

Dataset ID	Type of Data	Criteria	Release Date
JGAS000199	NGS (Exome)	Controlled-access (Type I)	2019/12/20
JGAS000237	NGS (WGS, RNA-seq)	Controlled-access (Type I)	2020/10/06
JGAS000256	NGS (RNA-seq)	Controlled-access (Type I)	2020/11/20
JGAS000378	NGS (RNA-seq, ChIP-seq)	Controlled-access (Type I)	2021/11/19
JGAS000350	NGS (RNA-seq)	Controlled-access (Type I)	2022/06/06
JGAS000550	NGS (scRNA-seq, RNA-seq, Exome)	Controlled-access (Type I)	2022/08/05
JGAD000687	Processed data of JGAD000335 by JGA	Controlled-access (Type I)	2022/12/27
JGAS000719	NGS（Exome, RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq）	Controlled-access (Type I)	2024/08/28
JGAS000881	NGS（Exome, RNA-seq）	Controlled-access (Type I)	2026/04/21

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

Exome (JGAS000199/JGAS000550/JGAS000719)

Participants/Materials	gastrointestinal inflammatory disease (ICD10: K51): 29 cases gastrointestinal inflammatory disease with neoplastic disease (ICD10: K51, C18, C19, C20): 26 cases organoids derived from healthy normal colonic tissues with neoplastic disease (ICD10: C18): 2 cases controls who underwent colonoscopy: 16 individuals pancreatic cancer (ICD10: C25): 50 cases 　(organoids derived from tumor tissues）
Targets	Exome
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 2500/4000, NovaSeq6000]
Library Source	DNAs extracted from peripheral blood cells and organoids established from normal or inflammatory/tumor tissues of the patients or controls
Cell Lines	-
Library Construction (kit name)	SureSelect Human All Exon kit
Fragmentation Methods	Ultrasonic fragmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	200 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000284 JGAD000669 JGAD000852
Total Data Volume	JGAD000284: 488 GB (fastq) JGAD000669: 59.5 GB (fastq) JGAD000852：846.3 GB（fastq）
Comments (Policies)	NBDC policy

 

WGS (JGAS000237)

Participants/Materials	Neoplastic disease: 23 cases (55 samples)     Small cell lung cancer (ICD10: C34)     Biliary tract cancer (ICD10: C23, C24, C78)     Colon cancer (ICD10: C18-20)     Duodenal cancer (ICD10: C17)     Esophageal cancer (ICD10: C15)     Stomach cancer (ICD10: C16, C78)     Liver cancer (ICD10: C22)     Pancreatic cancer (ICD10: C25)
Targets	WGS
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq X Ten]
Library Source	DNAs extracted from peripheral blood cells and organoids established from normal and cancer tissues of the patients
Cell Lines	-
Library Construction (kit name)	Library was constructed by BGI
Fragmentation Methods	Ultrasonic fragmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	300 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000335
Dataset ID of the Processed data by JGA	JGAD000687 The way to Process
Total Data Volume	2.752 TB (fastq)
Comments (Policies)	NBDC policy

 

RNA-seq (JGAS000237, JGAS000378)

Participants/Materials	Neoplastic disease: 23 + 4 cases (35+ 5 samples)     Small cell lung cancer (ICD10: C34)     Biliary tract cancer (ICD10: C23, C24, C78)     Colon cancer (ICD10: C18-20)     Duodenal cancer (ICD10: C17)     Esophageal cancer (ICD10: C15)     Stomach cancer (ICD10: C16, C78)     Liver cancer (ICD10: C22)     Pancreatic cancer (ICD10: C25)
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 2500/X Ten, NovaSeq 6000]
Library Source	RNAs extracted from organoids established from tumor tissues and a normal epithelial tissue of the patients RNAs extracted from organoids with BET bromodomain inhibitor established from tumor tissues and a normal epithelial tissue of colon cancer patients
Cell Lines	-
Library Construction (kit name)	TruSeq RNA Library Prep Kit v2 TruSeq Stranded mRNA Library Prep Kit
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	250 bp/150 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000336 JGAD000492
Total Data Volume	JGAD000336: 2.752 TB (fastq) JGAD000492: 190.5 GB (fastq)
Comments (Policies)	NBDC policy

 

RNA-seq (JGAS000256)

Participants/Materials	Neoplastic disease (ICD10: C16): 1 case (1 sample)
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq X Ten]
Library Source	Total RNA extracted from normal duodenum organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation
Cell Lines	-
Library Construction (kit name)	TruSeq RNA Library Prep Kit v2 TruSeq Stranded mRNA Library Prep Kit
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	250 bp/150 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000359
Total Data Volume	37 GB (fastq)
Comments (Policies)	NBDC policy

 

RNA-seq (JGAS000350)

Participants/Materials	Neoplastic disease (ICD10: C16): 2 cases (11 samples)
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 4000]
Library Source	RNAs extracted from organoids derived from colon cancer tissues
Cell Lines	-
Library Construction (kit name)	TruSeq RNA Library Prep Kit v2 TruSeq Stranded mRNA Library Prep Kit
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	250 bp/150 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000464
Total Data Volume	108.9 GB (fastq)
Comments (Policies)	NBDC policy

 

RNA-seq (JGAS000550)

Participants/Materials	Neoplastic disease (ICD10: C18): 2 cases (8 samples)
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [NovaSeq 6000]
Library Source	Total RNA extracted from normal duodenum organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation
Cell Lines	-
Library Construction (kit name)	TruSeq RNA Library Prep Kit v2 TruSeq Stranded mRNA Library Prep Kit
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 x 2 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000669
Total Data Volume	46.6 GB (fastq)
Comments (Policies)	NBDC policy

 

RNA-seq (JGAS000719)

Participants/Materials	Pancreatic cancer (ICD10: C25): 40 cases (50 samples)         organoids derived from tumor tissues: 38 cases (38 samples)         genetically engineered pancreatic duct organoids: 2 cases (12 samples)
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 4000, NovaSeq 6000]
Library Source	RNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids
Cell Lines	-
Library Construction (kit name)	TruSeq RNA Library Prep Kit v2 TruSeq Stranded mRNA Library Prep Kit
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 x 2 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000852
Total Data Volume	846.3 GB (fastq)
Comments (Policies)	NBDC policy

 

scRNA-seq (JGAS000550)

Participants/Materials	Neoplastic disease (ICD10: C16): 1 case (1 sample)
Targets	scRNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 4000]
Library Source	RNAs extracted from organoids from normal colonic tissue
Cell Lines	-
Library Construction (kit name)	Single Cell 3′ Library & Gel Bead Kit v2 and the A Chip Kit (10X Genomics)
Fragmentation Methods	Enzymatic fragmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	28+91 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000669
Total Data Volume	66.0 GB (fastq)
Comments (Policies)	NBDC policy

 

scRNA-seq (JGAS000719)

Participants/Materials	Pancreatic cancer (ICD10: C25): 1 case (6 samples) 　(genetically engineered pancreatic duct organoids)
Targets	scRNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 4000]
Library Source	RNAs extracted from genetically engineered pancreatic duct organoids
Cell Lines	-
Library Construction (kit name)	Chromium Next GEM Single Cell 3’ Reagent Kits v3.1
Fragmentation Methods	Enzymatic fragmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	28+91 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000852
Total Data Volume	846.3 GB (fastq)
Comments (Policies)	NBDC policy

 

ChIP-seq (JGAS000378)

Participants/Materials	Neoplastic disease: 4 cases (5 samples)     Colon cancer (ICD10: C18)
Targets	ChIP-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq X Ten]
Library Source	DNAs extracted from organoids derived from colon cancer tissues and a normal epithelial tissue of the patients, and immunoprecipitated with an anti-histone antibody (H3K27Ac)
Cell Lines	-
Library Construction (kit name)	Illumina Tagment DNA TDE1 Enzyme and Buffer Kits
Fragmentation Methods	Ultrasonic fragmentation (Bioruptor Ⅱ)
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000492
Total Data Volume	190.5 GB (fastq)
Comments (Policies)	NBDC policy

 

 

ChIP-seq (JGAS000719)

Participants/Materials	Pancreatic cancer (ICD10: C25): 5 cases (13 samples)         organoids derived from tumor tissues: 3 cases (3 samples)         genetically engineered pancreatic duct organoids: 2 cases (10 samples)
Targets	ChIP-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq X Ten]
Library Source	DNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids, and immunoprecipitated with an anti-histone antibody (H3K27me3)
Cell Lines	-
Library Construction (kit name)	Illumina Tagment DNA TDE1 Enzyme and Buffer Kits
Fragmentation Methods	Ultrasonic fragmentation (Bioruptor Ⅱ)
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 bp
QC	FRiP score
Mapping Methods	Bowtie2
Reference Genome Sequence	hg38
Peak Calling Methods (software)	MACS2
Japanese Genotype-phenotype Archive Dataset ID	JGAD000852
Total Data Volume	882.8 GB (fastq, bed)
Comments (Policies)	NBDC policy

 

ATAC-seq

Participants/Materials	Pancreatic cancer (ICD10: C25): 12 cases (16 samples)         organoids derived from tumor tissues: 10 cases (12 samples)         genetically engineered pancreatic duct organoids: 2 cases (4 samples)
Targets	ATAC-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq X Ten]
Library Source	DNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids
Cell Lines	-
Library Construction (kit name)	Omni-ATAC protocol
Fragmentation Methods	Tn5 transposase
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 x 2 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000852
Total Data Volume	846.3 GB (fastq)
Comments (Policies)	NBDC policy

 

Exome (JGAS000881)

Participants/Materials	Duodenal adenoma (ICD10: D13.2): 3 cases (6 samples)         organoids derived from duodenal tumor tissues: 3 cases (3 samples)         organoids derived from normal duodenal tissues: 3 cases (3 samples)
Targets	Exome
Target Loci for Capture Methods	-
Platform	Illumina [NovaSeq 6000]
Library Source	DNAs extracted from organoids established from tumor and normal tissues
Cell Lines	-
Library Construction (kit name)	SureSelect Human All Exon V6
Fragmentation Methods	Ultrasonic fragmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD001024
Total Data Volume	186.3 GB (fastq)
Comments (Policies)	NBDC policy

 

RNA-seq (JGAS000881)

Participants/Materials	Colon cancer (ICD10: C18): 3 cases (22 samples)         organoids derived from normal ileum tissues: 2 cases (6 samples)         genetically engineered normal ileum organoids: 2 cases (12 samples)         organoids derived from normal colon tissues: 1 case (2 samples)         genetically engineered normal colon organoids: 1 case (2 samples) Duodenal adenoma (ICD10: D13.2): 3 cases (12 samples)         organoids derived from duodenal tumor tissues: 3 cases (6 samples)         organoids derived from normal duodenal tissues: 3 cases (6 samples) Stomach cancer (ICD10: C16): 1 case (4 samples)         organoids derived from normal duodenal tissues: 1 case (2 samples)         genetically engineered normal duodenal organoids: 1 case (2 samples) 1 healthy individual         organoids derived from normal duodenal tissues: 1 case (2 samples)         genetically engineered normal duodenal organoids: 1 case (2 samples)
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [NovaSeq 6000]
Library Source	RNAs extracted from organoids established from tumor and normal tissues or genetically engineered organoids
Cell Lines	-
Library Construction (kit name)	TruSeq RNA Library Prep Kit v2
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD001024
Total Data Volume	186.3 GB (fastq)
Comments (Policies)	NBDC policy

 

 

DATA PROVIDER

Principal Investigator: Toshiro Sato

Affiliation: Department of Organoid Medicine, Keio University School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

Name	Title	Project Number
Project for Elucidating and Controlling Mechanisms of Aging and Longevity, Japan Agency for Medical Research and Development (AMED)	Understanding changes in aging traits aimed at controlling the onset of gastrointestinal diseases	JP19gm5010002
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED)	Development of advanced drug discovery system based on understanding of cancer multi-level phenotype	JP19cm0106206
Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST)	Dissecting intestinal fibrogenic diseases by a newly developed 4D disease model system	JP19gm1210001
KAKENHI Grant-in-Aid for Scientific Research (S)	Gaining Integrative Understanding of Gastrointestinal Disease Phenotypes through Establishment of an Organoid Library	17H06176
KAKENHI Grant-in-Aid for Scientific Research (B)	Functional analysis of small intestinal epithelial organoid-based transplant graft	20H03746
KAKENHI Grant-in-Aid for Scientific Research (S)	Elucidating a role of niche construction in pathophysiological mechanism of human digestive diseases	22H04995

 

PUBLICATIONS

	Title	DOI	Dataset ID
1	Somatic inflammatory gene mutations in human ulcerative colitis epithelium	doi: 10.1038/s41586-019-1844-5	JGAD000284
2	An Organoid Biobank of Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping	doi: 10.1016/j.cell.2020.10.023	JGAD000335 JGAD000336
3	An organoid-based organ repurposing approach to treat short bowel syndrome	doi: 10.1038/s41586-021-03247-2	JGAD000359
4	Organoid screening reveals epigenetic vulnerabilities in human colorectal cancer	doi: 10.1038/s41589-022-00984-x	JGAD000492
5

 

USRES (Controlled-access Data)

Principal Investigator	Affiliation	Country/Region	Research Title	Data in Use (Dataset ID)	Period of Data Use
Klaus H. Kaestner	Institue for Diabetes, Obesity & Metabolism at Unversity of Pennsylvania		Somatic mutation analysis of the pancreas in type 1 diabetes	JGAD000284	2020/04/13-2021/03/03
Ulf Leser	Department of Mathematics and Computer Science, Humboldt-Universitaet zu Berlin		MAPTor-NET: MAPK-mTOR network model driven individualized therapies of pancreatic neuro-endocrine tumors (pNETs)	JGAD000335, JGAD000336	2021/06/03-2023/04/01
Nobuhiro Tanuma	Miyagi Cancer Center Research Institute	Japan	Study on biological characters of pancreatic and gastrointestinal neuroendocrine tumors using patient-derived organoids.	JGAD000336	2022/09/19-2023/07/31
Michiaki Hamada	Faculty of Science and Engineering, Waseda University	Japan	Construction of RNA-targeted Drug Discovery Database	JGAD000336, JGAD000359, JGAD000492	2022/12/26-2025/03/31
Takuya Yamamoto	Laboratory of Precision Immunology, National Institutes of Biomedical Innovation, Health and Nutrition	Japan	Basic research for vaccine development against gastrointestinal cancer and malignant melanoma based on the identification of novel cancer antigens	JGAD000852	2024/11/12-2026/03/31
Kenichi Yoshida	Division of Cancer Evolution, National Cancer Center Research Institute	Japan	A multicenter study on genomic analysis of solid tumors	JGAD000852	2025/09/19-2028/03/31

NBDC Research ID: hum0536.v1

 

SUMMARY

Aims: Malignant pleural mesothelioma is an aggressive pleural tumor with poor prognosis. Understanding the molecular mechanisms underlying its development and progression is essential for improving diagnosis and treatment. This study aims to identify clinically relevant molecular pathways through genomic and transcriptome analyses of tumor and non-tumor pleural tissues. Candidate genes associated with tumor initiation and progression will be analyzed in terms of gene expression, localization, dynamics, and cell-to-cell interactions. Their correlation with clinicopathological parameters will also be investigated. Tumor tissues will be preserved by cryopreservation or transplantation into immunodeficient mice to enable further studies using in vivo models or in vitro cell culture systems.

Methods: WGS, single-cell RNA-seq, ATAC-seq

Participants/Materials: One pleural mesothelioma patient

Dataset ID	Type of Data	Criteria	Release Date
JGAS000859	NGS (WGS, scRNA-seq, ATAC-seq)	Controlled-access (Type I)	2026/04/08

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

WGS

Participants/Materials:	Pleural mesothelioma (ICD10: C45.0): 1 case       tumor tissues: 2 samples
Targets	WGS
Target Loci for Capture Methods	-
Platform	Illumina [NovaSeq 6000]
Library Source	DNAs extracted from tumor tissues
Cell Lines	-
Library Construction (kit name)	Illumina DNA PCR-Free Prep Kit
Fragmentation Methods	Transposome-mediated on-bead tagmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 bp x 2
Japanese Genotype-phenotype Archive Dataset ID	JGAD001002
Total Data Volume	680.3 GB (fastq)
Comments (Policies)	NBDC policy

 

single-nucleus RNA-seq

Participants/Materials:	Pleural mesothelioma (ICD10: C45.0): 1 case       tumor tissue: 1 sample       Patient-derived xenograft (PDX) tumor model specimen: 2 samples
Targets	scRNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [NovaSeq 6000]
Library Source	RNAs extracted from enzymatically dissociated tumor samples
Cell Lines	-
Library Construction (kit name)	Chromium Single Cell 5' Reagent Kits v2 Dual Index, Library Construction Kit
Fragmentation Methods	Enzymatic fragmentation
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	Read1: 26 bp, Read2: 90bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD001002
Total Data Volume	680.3 GB (fastq)
Comments (Policies)	NBDC policy

 

ATAC-seq

Participants/Materials:	Pleural mesothelioma (ICD10: C45.0): 1 case       Patient-derived cell line: 2 samples
Targets	ATAC-seq
Target Loci for Capture Methods	-
Platform	Illumina [NovaSeq 6000]
Library Source	DNAs extracted from cell line
Cell Lines	-
Library Construction (kit name)	ATAC-Seq Kit（Active Motif）
Fragmentation Methods	included in the above library construction kit
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	150 bp x 2
Japanese Genotype-phenotype Archive Dataset ID	JGAD001002
Total Data Volume	680.3 GB (fastq)
Comments (Policies)	NBDC policy

 

DATA PROVIDER

Principal Investigator: Shumpei Ishikawa

Affiliation: Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo

Project / Group Name: -

Funds / Grants (Research Project Number):

Name	Title	Project Number
KAKENHI Grant-in-Aid for Scientific Research (S)	A New Definition of Heterogeneity in Gastric Cancer through Quantitative Integration of Spatial Tissue and Genomic Information	22H04990
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED)	Trajectory Analysis of Genomic and Pathological Information during the Treatment Course of Refractory Cancers	JP24ck0106904
KAKENHI Grant-in-Aid for Scientific Research (B)	Elucidation of a Novel Neutrophil–Tumor Interaction in Diffuse-Type Gastric Cancer	23K27436
KAKENHI Grant-in-Aid for JSPS Fellows	Mechanistic Dissection of Tumor–Stromal Interactions and Identification of Therapeutic Targets in Malignant Pleural Mesothelioma	23KJ0836

 

PUBLICATIONS

	Title	DOI	Dataset ID
1	Cooperative Response Loops Enhanced by Histamine Signaling during Tumor-Neutrophil Crosstalk in Pleural Mesothelioma		JGAD001002

 

USRES (Controlled-access Data)

Principal Investigator	Affiliation	Country/Region	Research Title	Data in Use (Dataset ID)	Period of Data Use