NBDC Research ID: hum0486.v1
SUMMARY
Aims: Biliary atresia (BA) is a poor prognosis disease that causes fibrotic obstruction of the extrahepatic bile ducts by early infancy and progresses from bile stagnation to cirrhosis, the cause of which is still unknown. The aim of this study is to establish a bile duct cell induction system from normal human iPS cells and to prove the abnormality during the fetal period. Using this system, we will elucidate the molecular mechanisms of bile duct formation after mid-development, establish stable long-term culture techniques for bile duct stem cells, construct bile duct tree structures through in vitro and in vivo experiments, and establish an experimental system to investigate the bile duct injury process using biliary atresia-specific iPS cells.
Methods: whole genome sequencing (WGS)
Participants/Materials: iPS cell samples generated from five patients with biliary atresia (type I cyst)
URL: https://acd.brc.riken.jp/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000765 | NGS (WGS) | Controlled-access (Type I) | 2024/11/29 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
biliary atresia (type I cyst) (ICD10: Q44.2): 5 cases iPS cells generated from PBMCs: 5 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq X Plus 25B] |
| Library Source | DNAs extracted from iPS cells |
| Cell Lines | - |
| Library Construction (kit name) | Illumina DNA PCR-Free Prep |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | CLC Genomics Workbench version 20 |
| Mapping Quality | Q30 > 80% |
| Reference Genome Sequence | GRCh37 - hg19 |
| Coverage (Depth) | > 30 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000906 |
| Total Data Volume | 314.2 GB (fastq, csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yohei Hayashi
Affiliation: RIKEN BioResource Research Center
Project / Group Name: iPS Cell Advanced Characterization and Development Team
URL: https://acd.brc.riken.jp/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Generation of human induced pluripotent stem cell lines derived from patients of cystic biliary atresia | doi: 10.1007/s13577-024-01147-x | JGAD000906 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
