Research ID
hum0231-v2Release info
Latest
Research title
A study for the establishment of disease-specific iPS cells.
Research overview
- Aims
- We receive patient samples and information from various diseases, as well as samples from healthy controls serving as reference groups, from collaborating medical institutions. At our university, we establish human iPS cells from these samples. After evaluating their characteristics, we deposit these cells in a bank, maintaining and expanding the collection. This enables us to advance disease-specific iPS cell research into disease causation, disease treatment, disease analysis, and therapeutic development. It also facilitates the analysis of disease pathologies and the development of treatments, while establishing a research infrastructure.
- Methods
- WES
DNA extracted from PBMC was fragmented using a ultrasonicator, and libraries were prepared using the SureSelect Human All Exon V6 (Agilent Technologies). Sequencing was carried out on a HiSeq 2500 system (Illumina) with 100-bp pair-end reads.
RNA-seq
Reverse transcription was performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). The resulting cDNA was fragmented using a Covaris Focused-ultrasonicator M220 (M&S Instruments Inc.), and libraries were prepared using the SMARTer ThruPLEX DNA-seq Kit (Takara). Sequencing was carried out on a NextSeq 500 system (Illumina) with 75-bp single-end reads.
ChIP-seq
Cells were cross-linked with 1% formaldehyde solution, and genomic DNA was fragmented. The samples were incubated overnight at 4 °C with magnetic beads conjugated with 2.5 μg of antibody. After washing, reverse cross-linking was performed at 65 °C. Libraries were prepared using the SMARTer ThruPLEX DNA-seq Kit (Takara) and sequenced on a NextSeq 500 system (Illumina) with 75-bp single-end reads. - Participants/materials
- PBMC from 120 healthy donors, Monocytes and macrophages differentiated from iPS cells (including genome-edited strains) derived from 2 healthy donors
- URL
- N/A
Datasets
| Cart | Dataset ID | Type of data | Platforms | Access criteria | Date published |
|---|---|---|---|---|---|
| JGAD000393 | NGS (Exome) |
| Controlled-access (Type I) | 2024-07-23 | |
| JGAD000989 | NGS （RNA-seq, ChIP-seq） |
| Controlled-access (Type I) | 2026-11-06 |
Data provider
- Principal investigator
- Megumu K. Saito
- Affiliation
- Center for iPS cell resarch and application, Kyoto University
Research projects
No research projects.
Grants
| Name | Title | Project number |
|---|---|---|
The Program for Intractable Diseases Research utilizing Disease-specific iPS cells, Japan Agency for Medical Research and Development (AMED) | Fundamental research of promote establishment of disease-specific iPS cells |
|
The Program for Intractable Diseases Research utilizing Disease-specific iPS cells, Japan Agency for Medical Research and Development (AMED) | Construction of comprehensive iPSC library on Japanese healthy donors |
|
iPS cell research fund, Center for iPS cell research and application, Kyoto university | N/A | N/A |
The Uehara Memorial Foundation | iPSC-based functional dissection of COVID-19 severity-associated SNPs | N/A |
The Kurata Grants by The Hitachi Global Foundation | iPSC-based functional dissection of COVID-19 severity-associated SNPs | N/A |
iPS Academia Japan | iPSC-based functional dissection of COVID-19 severity-associated SNPs | N/A |
Acceleration Program of R&D and Implementation for Regenerative Medicine and Cell and Gene Therapy & Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED) | Research on the expansion of an iPS cell bank for rare diseases, focusing on designated intractable diseases |
|
Acceleration Program of R&D and Implementation for Regenerative Medicine and Cell and Gene Therapy, Japan Agency for Medical Research and Development (AMED) | Joint Research Support Program for Promoting Disease Research using iPS Cells |
|
Acceleration Program of R&D and Implementation for Regenerative Medicine and Cell and Gene Therapy, Japan Agency for Medical Research and Development (AMED) | Core Research Center for Next-generation Medicine Utilizing Cell and Gene Therapy |
|
Related publications
| Title | DOI | Dataset ID |
|---|---|---|
iPSC-based functional genomics reveals functionally opposing variants within a disease-associated haplotype |
Controlled access users
No use of the controlled access data has been recorded.