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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

JGAD000633

Type of data
NGS (RNA-seq, ChIP-seq, Hi-C)
Access criteria
Controlled-access (Type I)
Total data volume
618 GB
File formats
  • FASTQ
  • BED
  • narrowPeak
  • bigWig
  • HIC
  • TXT
Research
hum0257
Date published
2023-01-05
Date modified
2023-01-05
DDBJ Search
JGAD000633 (opens in a new tab)
JGA Study
JGAS000514 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 10 cases
One case of organoid from tumor tissues with HNF1B overexpression (2 samples) and its control (2 samples)
  • Health status
    Affected
  • Subject count
    15 (Individual)
Disease
Pancreatic ductal adenocarcinoma (C253)
Sample description
RNAs extracted from organoids established from pancreatic tumors
  • Tissue
    Organoid
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq RNA Library Prep Kit
TruSeq Stranded mRNA Library Prep Kit
Fragmentation
Heat treatment
Platform
Illumina HiSeq 2500
Illumina NovaSeq 6000
Read type
Paired-end
Read length
100 bp
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)

ChIP-seq

Materials and participants
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 2 cases
[JGAD000633/GSE202023] organoids derived from tumor tissues: 6 samples (with/without HNF1B overexpression with anti-CTCF antibody, anti-H3K27Ac antibody or anti-HNF1B antibody)
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
Pancreatic ductal adenocarcinoma (C253)
Sample description
Chromatin immunoprecipitated DNAs extracted from organoids established from pancreatic tumors
  • Tissue
    Organoid
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
ChIP-seq
Target
N/A
Reagent kit
Illumina Tagment DNA TDE1 Enzyme and Buffer Kits
Fragmentation
Ultrasonic fragmentation (Bioruptor UCD-250)
Platform
Illumina NextSeq 500
Read type
Single-end
Read length
75 bp
Gene Expression Omnibus Accession
GSE202023
Data use policy
NBDC data sharing policy (JGAP000001)

Hi-C

Materials and participants
Pancreatic ductal adenocarcinoma (ICD10: C25.3): 2 cases
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
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
Pancreatic ductal adenocarcinoma (C253)
Sample description
Cross-linked DNAs extracted from organoids established from pancreatic tumors
  • Tissue
    Organoid
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Hi-C
Target
N/A
Reagent kit
Arima Hi-C Kit
Fragmentation
Enzymatic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)