NBDC Research ID: hum0508.v1
SUMMARY
Aims: We will establish disease-specific iPS cells from patient somatic cells and induce them into an ocular developmental model system to mimic the ocular developmental stage in vitro, and conduct detailed analysis of the phenotype and cell population obtained at the time of differentiation induction, which is extrapolated to the normal stage of formation of major organs. This research will help to elucidate the pathogenesis of the disease and to search for therapeutic methods. This research is expected to elucidate the detailed pathogenesis and mechanisms of ocular diseases that have remained unexplored until now.
Methods: single-cell RNA-seq
Participants/Materials: Epithelial tissues were collected from the clear central corneal region and the limbus of a patient with congenital aniridia during cultivated oral mucosal epithelial transplantation (COMET) surgery. The tissues were obtained by gentle scraping using a scalpel.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000790 | NGS (scRNA-seq) | Controlled-access (Type I) | 2025/06/04 |
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MOLECULAR DATA
| Participants/Materials |
congenital aniridia (ICD10: Q131): 1 case corneal and limbal epithelial cells: 2 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from corneal and limbal epithelial cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit v2 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 90 bp |
| Mapping Methods | Cell Ranger (10x Genomics, v7.1.0) |
| Mapping Quality | Reads Mapped to Genome: 93.5% (CE), 94.7% (LE) |
| Reference Genome Sequence | GRCh38 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000932 |
| Total Data Volume | 113.7 GB (fastq, bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kohji Nishida
Affiliation: Department of Ophthalmology, Graduate School of Medicine, Osaka University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED) | Stem cell system-based four dimensional ocular tissue remodeling in homeostatic and pathological states | JP18gm1210004 |
| Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED) | Elucidation of pathogenesis and development of therapeutics in aniridia using disease-specific iPS cells | JP22bm0804021 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Transcriptional landscape of aniridia-associated keratopathy through single-cell RNA sequencing | doi: 10.1016/j.jtos.2025.05.008 | JGAD000932 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
