NBDC Research ID: hum0302.v2
SUMMARY
Aims: To characterize iPS cell lines (healthy-donor iPS cell lines and disease-specific iPS cell lines), differentiation potential analysis (evaluation of differentiation potential into disease-causing cells and involved cells), disease-causing gene analysis, and whole genome analysis were performed.
Methods:
[JGAS000382] Hepatocytes were induced to differentiate from human iPS cells and collected on day 19. RNA was collected and strand-specific library preparation was performed by a PolyA selection method. The prepared library was sequenced by Novaseq6000. Sequencing was performed in a 2x150 bp PE configuration with a data output of about 6 Gb per sample (equivalent to about 20 million paired reads).
[JGAS000683] Kidney organoids were induced to differentiate from human iPS cells and collected on day 18. RNA was collected and strand-specific library preparation was performed by a PolyA selection method. The prepared library was sequenced by Novaseq6000. Sequencing was performed in a 2x150 bp PE configuration with a data output of about 6 Gb per sample (equivalent to about 20 million paired reads).
Participants/Materials: iPS cells derived from patients with Wilson's disease, juvenile nephron tabes (NPH1) patients and iPS cells derived from healthy donors
URL: https://acd.brc.riken.jp/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000382 | NGS (RNA-seq) | Controlled-access (Type I) | 2022/09/05 |
| JGAS000683 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/03/18 |
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MOLECULAR DATA
| Participants/Materials |
[JGAS000382] Five samples of hepatocytes differentiated from iPS cells derived from patients with Wilson's disease (ICD10: E830) One hepatocyte sample from a patient with Wilson's disease in which the ATP7B mutation was corrected by genome editing of iPS cells Five samples of hepatocytes differentiated from healthy human-derived iPS cells One hepatocyte sample in which the ATP7B mutation was introduced by genome editing of healthy donor-derived iPS cells [Total: 12 samples] [JGAS000683] 6 kidney organoid samples induced from juvenile nephron tabes (NPH1) patient-derived iPS cells (ICD10: N19) 6 kidney organoid samples induced from juvenile nephron tabes (NPH1) patient-derived iPS cells overexpressing the responsible gene NPHP1 3 kidney organoid samples induced to differentiate from healthy human iPS cells 3 kidney organoid samples in which NPHP1 mutation was introduced by genome editing of healthy human iPS cells [Total: 18 samples] |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from hepatocytes and kidney organoids differentiated from iPS cells |
| Cell Lines | - |
| Library Construction (kit name) | GeneWiz inc.'s protocol |
| Fragmentation Methods | GeneWiz inc.'s protocol |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume | 45.6 + 72.9 GB (fastq) |
| 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 | Retinoids rescue ceruloplasmin secretion and alleviate oxidative stress in Wilson's disease-specific hepatocytes. | doi: 10.1093/hmg/ddac080 | JGAD000497 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
