NBDC Research ID: hum0249.v2
SUMMARY
Aims: Elucidation of pathological conditions and development of therapeutic methods using iPS cells derived from patients with hard tissue/connective tissue related diseases
Methods: Cap Analysis of Gene Expression (CAGE)-seq, single-cell RNA-seq, and CUT＆RUN-seq
Participants/Materials: iPS cells derived from patients with hard tissue/connective tissue related diseases (genetic defect in RUNX2 positive)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000248 | NGS (CAGE-seq) | Controlled-access (Type I) | 2020/09/01 |
| JGAS000663 | NGS (scRNA-seq, CUT＆RUN-seq) | Controlled-access (Type I) | 2025/03/21 |
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MOLECULAR DATA
| Participants/Materials |
hard tissue/connective tissue related diseases (ICD10: Q870): 3 cases osteoblast differentiated from iPS cells established from oral mucosa fibroblast: 2 cases (2 samples) osteoblast differentiated from iPS cells established from oral mucosa fibroblast (mutation-corrected iPS cells by gene editing): 1 case (1 sample) |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source | RNA extracted from osteoblast differentiated from iPS cells |
| Cell Lines | - |
| Library Construction (kit name) | nAnT-iCAGE protocol |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 47 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000348 |
| Total Data Volume | 39 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hard tissue/connective tissue related diseases (ICD10: Q870): 2 cases iPSCs derived from oral mucosa of a fibroblast patient with Cleidocranial Dysostosis (CCD) (mutation-corrected iPS cells by gene editing) : 1 case (1 sample) osteoblast differentiated from iPSCs derived from oral mucosa of a fibroblast patient with Cleidocranial Dysostosis (CCD) (mutation-corrected iPS cells by gene editing): 1 case (1 sample) iPSCs derived from oral mucosa of a fibroblast patient with Cleidocranial Dysostosis (CCD) (RUNX2 knocked out iPS cells by gene editing): 1 case (1 sample) osteoblast differentiated from iPSCs derived from oral mucosa of a fibroblast patient with Cleidocranial Dysostosis (CCD) (RUNX2 knocked out iPS cells by gene editing): 1 case (1 sample) osteoblast differentiated from iPSCs derived from oral mucosa of a fibroblast patient with Cleidocranial Dysostosis (CCD) (RUNX2 knocked out iPS cells by gene editing) with forced expression of SYNE1: 1 case (1 sample) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNA extracted from iPS cells and osteoblast differentiated from iPS cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000793 |
| Total Data Volume | 474 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hard tissue/connective tissue related diseases (ICD10: Q870): 2 cases osteoblast differentiated from iPS cells established from oral mucosa fibroblast: 2 cases (2 samples) osteoblast differentiated from ips cells established from oral mucosa fibroblast (mutation-corrected ips cells by gene editing): 1 case (1 sample) |
| Targets | CUT＆RUN-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from osteoblast differentiated from iPS cells |
| Cell Lines | - |
| Library Construction (kit name) | CUT&RUN Library Prep Kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000793 |
| Total Data Volume | 474 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshifumi Azuma
Affiliation: Tokyo Dental College / Biochemistry
Project / Group Name:Tokyo Dental College Research Branding Project
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | The osteoblast differentiation control mechanism based on a new concept | 19K10063 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | The osteoblast differentiation and calcification mechanism of GNAS-cAMP pathway using diseased iPS cells | 18H03007 |
| Tokyo Dental College Research Branding Project |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | CAGE-seq analysis of osteoblast derived from cleidocranial dysplasia human induced pluripotent stem cells | doi: 10.1016/j.bone.2020.115582 | JGAD000348 |
| 2 | Intracellular tension generated by RUNX2-induced LINC complex formation creates a nuclear environment essential for bone differentiation | JGAD000793 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
