NBDC Research ID: hum0201.v1
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SUMMARY
Aims: Search for differences in genomics and traits among normal cells, digestive non-tumor cells (inflammatory cells), and tumor cells
Methods: 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.
Participants/Materials: Controls who underwent colonoscopy, gastrointestinal inflammatory disease patients, and neoplastic disease patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000199 | NGS (Exome) | Controlled-access (Type I) | 2019/12/20 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
gastrointestinal inflammatory disease (ICD10: K51): 29 cases gastrointestinal inflammatory disease with neoplastic disease (ICD10: K51, C18, C19, C20): 26 cases controls who underwent colonoscopy: 16 individuals |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500/4000] |
| Library Source | DNAs extracted from inflammatory/tumor tissues, peripheral blood cells, and organoids established from epithelial tissues of the patients |
| 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 | JGAD000284 |
| Total Data Volume | 488 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 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Somatic inflammatory gene mutations in human ulcerative colitis epithelium | doi: 10.1038/s41586-019-1844-5 | JGAD000284 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
| Klaus H. Kaestner | Institue for Diabetes, Obesity & Metabolism at Unversity of Pennsylvania | JGAD000284 | 2020/04/13-2021/03/03 |
