NBDC Research ID: hum0257.v2
SUMMARY
Aims: Comprehensive analysis of human pancreatic tumor subtypes.
Methods: Whole Exome sequencing, RNA sequencing, ATAC sequencing, ChIP sequencing, and Hi-C analysis using organoids established from pancreatic tumors.
Participants/Materials: Pancreatic ductal adenocarcinoma, Intraductal papillary mucinous neoplasm
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000263 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2021/12/24 |
| E-GEAD-414 | NGS (RNA-seq) | Unrestricted-access | 2021/12/24 |
| JGAS000264 | NGS (ATAC-seq, ChIP-seq) | Controlled-access (Type I) | 2021/12/24 |
| E-GEAD-416 | NGS (ATAC-seq) | Unrestricted-access | 2021/12/24 |
| E-GEAD-417 | NGS (ChIP-seq) | Unrestricted-access | 2021/12/24 |
| JGAS000262 | NGS (Hi-C) | Controlled-access (Type I) | 2021/12/24 |
| E-GEAD-415 | NGS (Hi-C) | Unrestricted-access | 2021/12/24 |
| JGAS000514 | NGS (RNA-seq, ChIP-seq, Hi-C) | Controlled-access (Type I) | 2023/01/10 |
| GSE202023 | NGS (ChIP-seq) | Unrestricted-access | 2023/01/10 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
*When the research results including the data which were downloaded from GEA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include them in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 10 cases - organoids derived from tumor tissues: 10 samples Intraductal papillary mucinous neoplasm (ICD10: D13.6): 3 cases - organoids derived from tumor tissues: 3 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from organoids established from pancreatic tumors |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp, 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000366 |
| Total Data Volume | 121 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 10 cases [JGAD000366/E-GEAD-414] organoids derived from tumor tissues: 22 samples [JGAD000633] One case of organoid from tumor tissues with HNF1B overexpression (2 samples) and its control (2 samples) Intraductal papillary mucinous neoplasm (ICD10: D13.6): 5 cases [JGAD000366/E-GEAD-414] organoids derived from tumor tissues: 4 samples, organoids derived from tumor-adjacent tissues: 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500, NovaSeq 6000] |
| Library Source | RNAs extracted from organoids established from pancreatic tumors |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA sample Preparation KitV2, TruSeq Stranded mRNA LT Sample Prep Kit, TruSeq Stranded mRNA Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp, 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Genomic Expression Archive ID | E-GEAD-414 |
| Total Data Volume |
JGAD000366/E-GEAD-414: 121 GB (fastq) JGAD000633: 15 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 17 cases - organoids derived from tumor tissues: 20 samples Intraductal papillary mucinous neoplasm (ICD10: D13.6): 6 cases - organoids derived from tumor tissues: 4 samples, organoids derived from tumor-adjacent tissues: 2 samples |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source | DNAs extracted from organoids established from pancreatic tumors |
| Cell Lines | - |
| Library Construction (kit name) | Illumina Tagment DNA TDE1 Enzyme and Buffer Kits |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50 bp + 25 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000367 |
| Genomic Expression Archive ID | E-GEAD-416 |
| Total Data Volume | 117 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 2 cases [JGAD000367/E-GEAD-417] organoids derived from tumor tissues: 4 samples (2 ChIP experiments and 2 input experiments) [JGAD000633/GSE202023] organoids derived from tumor tissues: 6 samples (with/without HNF1B overexpression with anti-CTCF antibody, anti-H3K27Ac antibody or anti-HNF1B antibody) |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source | Chromatin immunoprecipitated DNAs extracted from organoids established from pancreatic tumors |
| Cell Lines | - |
| Library Construction (kit name) | Illumina Tagment DNA TDE1 Enzyme and Buffer Kits |
| Fragmentation Methods | Ultrasonic fragmentation (Bioruptor UCD-250) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Genomic Expression Archive ID | E-GEAD-417 |
| Gene Expression Omnibus ID | GSE202023 |
| Total Data Volume |
JGAD000367/E-GEAD-417: 117 GB (fastq) JGAD000633/GSE202023: 10 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 2 cases [JGAD000365] organoids derived from tumor tissues: 2 samples [JGAD000633] duplicate for each condition: 8 samples - One case of organoid from tumor tissues: with/without HNF1B overexpression - One case of organoid from tumor tissues of pancreatic ductal adenocarcinoma derived from intraductal papillary mucinous neoplasm: with/without HNF1B knockdown |
| Targets | Hi-C |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | Cross-linked DNAs extracted from organoids established from pancreatic tumors |
| Cell Lines | - |
| Library Construction (kit name) | Arima Hi-C kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Genomic Expression Archive ID | E-GEAD-415 |
| Total Data Volume |
JGAD000365: 159 GB (fastq) JGAD000633: 493 GB (fastq) |
| Comments (Policies) | NBDC policy |
*This study was supported by "Genome Science". "Genome Science" is a part of the "Support Programs for Three Fields in Life Sciences (cancer, genome, and brain sciences)" established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Keisuke Tateishi
Affiliation: Department of Gastroenterology, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Comprehensive biological network analysis of pancreatic cancer | 19K08435 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Stratification and optimization of pancreatic cancer treatment based on chromatin dynamics | 21K15966 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | MNX1-HNF1B axis is indispensable for intraductal papillary mucinous neoplasm lineages | doi: 10.1053/j.gastro.2021.12.254 | JGAD000365 JGAD000366 JGAD000367 E-GEAD-414 E-GEAD-415 E-GEAD-416 E-GEAD-417 |
| 2 | HNF1B-driven three-dimensional chromatin structure for molecular classification in pancreatic cancers | doi: 10.1111/cas.15690 | JGAD000633 GSE202023 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000366 | 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 | JGAD000366 | 2024/11/12-2025/09/01 |
