NBDC Research ID: hum0088.v2
SUMMARY
Aims: To elucidate the effect and its mechanism of BMP signaling on glioma initiating cells
Methods: Target genes were identified by RNA-seq to elucidate the mechanism of regulation of glioma initiating cells by BMP. Genomic DNA was extracted from glioma initiating cells and whole genome sequencing was performed.
Participants/Materials: Patient-derived glioblastoma cell lines (tumor initiating cells), 2 lines
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000077 | NGS (RNA-seq) | Controlled-access (Type I) | 2019/02/08 |
| JGAS000096 | NGS (WGS) | Controlled-access (Type I) | 2019/02/08 |
| JGAS000077 (Data addition) | NGS (RNA-seq) | Controlled-access (Type I) | 2019/09/10 |
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MOLECULAR DATA
| Participants/Materials | 2 glioblastomas (ICD10：C71.9) (TGS-01, TGS-04) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [Genome Analyzer IIx] Thermo Fisher Scientific [IonProton] |
| Library Source |
JGAD000077: mRNA extracted from glioblastoma cell lines (TGS-01, TGS-04) stimulated with BMP-4 for 24 h prior to RNA extraction JGAD000263: mRNA extracted from a glioblastoma cell line (TGS-01) infected with Ad-EPHA6(WT), Ad-EPHA6(K757R) or Ad-LacZ (MOI 60) with or without BMP-2 stimulation for 24 h prior to RNA extraction |
| Cell Lines | - |
| Library Construction (kit name) |
ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre） Ion Total RNA-seq Kit v2 (Thermo Fisher Scientific) |
| Fragmentation Methods |
Genome Analyzer IIx: Enzymatic fragmentation (included in the kit) IonProton: Enzymatic fragmentation (included in the kit: RNase III) |
| Spot Type |
Genome Analyzer IIx: Paired-end IonProton: Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Genome Analyzer IIx: 76 bp IonProton: 200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000077: 43 GB (fastq) JGAD000263: 50 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 1 glioblastoma (ICD10：C71.9) (TGS-01) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Thermo Fisher Scientific [IonProton] |
| Library Source | gDNA extracted from glioblastoma cell line (tumor initiating cells) |
| Cell Lines | - |
| Library Construction (kit name) |
Ion Fragment plus library Kit Ion PI Template OT2 200 Kit v3 Ion PI Sequencing 200 Kit v3 (Thermo Fisher Scientific) |
| Fragmentation Methods | Ultrasonic fragmentation (Bioruptor UCD-200) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000096 |
| Total Data Volume | 13 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kohei Miyazono
Affiliation: Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Effects of TGF-β family on cancer microenvironment and strategies for cancer therapy | 22112002 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Roles of BMP signaling in maintenance of cell stemness | 24390070 |
| KAKENHI Grant-in-Aid for Scientific Research (S) | Transcriptional regulation by TGF-β signaling and its relation to progression of cancer | 15H05774 |
| JSPS Core-to-Core Program | Cooperative International Framework in TGF-beta Family Signaling | - |
| KAKENHI Grant-in-Aid for Early-Career Scientists | EphA6 tyrosine kinase as a potential biomarker for BMP-based therapy in adult glioblastoma Research Project | 19K16735 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Molecular mechanisms of cell differentiation and diversity by TGF-beta family members | 17H06326 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Bone morphogenetic protein signaling mediated by ALK-2 and DLX2 regulates apoptosis in glioma-initiating cells. | doi: 10.1038/onc.2017.112 | JGAD000077 |
| 2 | Identification of a novel fusion gene HMGA2-EGFR in glioblastoma. | doi: 10.1002/ijc.31179 |
JGAD000077 JGAD000096 |
| 3 | Tyrosine kinase Eph receptor A6 sensitizes glioma-initiating cells towards bone morphogenetic protein-induced apoptosis. | doi: 10.1111/cas.14187 | JGAD000263 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database |
JGAD000077 JGAD000096 |
2022/12/26-2025/03/31 |
