NBDC Research ID: hum0201.v8
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.
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
| 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 |
*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 | |
| Total Data Volume |
JGAD000284: 488 GB (fastq) JGAD000669: 59.5 GB (fastq) JGAD000852：846.3 GB（fastq） |
| Comments (Policies) | NBDC policy |
| 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 | |
| Dataset ID of the Processed data by JGA | |
| 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 | |
| Total Data Volume |
JGAD000336: 2.752 TB (fastq) JGAD000492: 190.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| 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 |
| Participants/Materials | Neoplastic disease (ICD10: C16): 2 case (11 sample) |
| 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 |
| Participants/Materials | Neoplastic disease (ICD10: C18): 2 case (8 sample) |
| 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 |
| Participants/Materials |
Pancreatic cancer (ICD10: C25): 40 case (50 sample) 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 |
| 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 |
| Participants/Materials |
Pancreatic cancer (ICD10: C25): 1 case (6 sample) (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 |
| 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 |
| Participants/Materials |
Pancreatic cancer (ICD10: C25): 5 case (13 sample) 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 |
| 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 |
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 | 2024/11/12-2025/09/01 |
