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 IDType of DataCriteriaRelease 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

*Release Note

* 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

Exome

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

 

RNA-seq

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

JGAD000366

JGAD000633

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

 

ATAC-seq

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

 

ChIP-seq

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

JGAD000367

JGAD000633

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

 

Hi-C

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 Restriction enzyme treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000365

JGAD000633

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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