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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

JGAD000852

Type of data
NGS (Exome, RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq)
Access criteria
Controlled-access (Type I)
Total data volume
846 GB
File formats
  • FASTQ
  • BED
Research
hum0201
Date published
2024-08-30
Date modified
2024-08-30
DDBJ Search
JGAD000852 (opens in a new tab)
JGA Study
JGAS000719 (opens in a new tab)

Analysis method

WES

Materials and participants
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)
  • Health status
    Mixed
  • Subject count
    123 (Individual)
Disease
gastrointestinal inflammatory disease (K51)
gastrointestinal inflammatory disease with neoplastic disease (K51, C18, C19, C20)
neoplastic disease (C18)
pancreatic cancer (C25)
Sample description
DNAs extracted from peripheral blood cells and organoids established from normal or inflammatory/tumor tissues of the patients or controls
  • Tissue
    Colon, Organoid, Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon
Fragmentation
Ultrasonic fragmentation
Platform
Illumina HiSeq 2500
Illumina HiSeq 4000
Illumina NovaSeq 6000
Read type
Paired-end
Read length
200 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    50 (Sample)
Disease
Pancreatic cancer (C25)
Sample description
RNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids
  • Tissue
    Organoid, Pancreas
  • Tumor / normal
    Tumor
Cell line
Genetically engineered pancreatic duct organoid
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 4000
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)

scRNA-seq

Materials and participants
Pancreatic cancer (ICD10: C25): 1 case (6 samples)
(genetically engineered pancreatic duct organoids)
  • Health status
    Affected
  • Subject count
    6 (Sample)
Disease
Pancreatic cancer (C25)
Sample description
RNAs extracted from genetically engineered pancreatic duct organoids
  • Tissue
    Organoid, Pancreas
  • Tumor / normal
    Tumor
Cell line
Genetically engineered pancreatic duct organoid
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 3' v3.1
Fragmentation
Enzymatic fragmentation
Platform
Illumina HiSeq 4000
Read type
Paired-end
Read length
read1: 28 bp
read2: 91 bp
Data use policy
NBDC data sharing policy (JGAP000001)

ChIP-seq

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    13 (Sample)
Disease
Pancreatic cancer (C25)
Sample description
DNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids, and immunoprecipitated with an anti-histone antibody (H3K27me3)
  • Tissue
    Organoid, Pancreas
  • Tumor / normal
    Tumor
Cell line
Genetically engineered pancreatic duct organoid
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 Ⅱ)
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh38
Mapping
Bowtie2
QC and filtering
FRiP score
Analysis method
MACS2
Processed data type
Peak calls
Data use policy
NBDC data sharing policy (JGAP000001)

ATAC-seq

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    16 (Sample)
Disease
Pancreatic cancer (C25)
Sample description
DNAs extracted from pancreatic cancer organoids or genetically engineered pancreatic duct organoids
  • Tissue
    Organoid, Pancreas
  • Tumor / normal
    Tumor
Cell line
Genetically engineered pancreatic duct organoid
Sample provider
N/A
Experimental method
ATAC-seq
Target
N/A
Reagent kit
Omni-ATAC
Fragmentation
Tn5 transposase
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)