NBDC Research ID: hum0401.v1
SUMMARY
Aims: Sarcomas are classified as rare cancers, that is, cancers with an incidence of 6/100000 patients per year. The prognosis of rare cancers, including sarcomas, is poorer than that of common cancers because of the lack of effective treatment. One of the reasons is that the biological resources of sarcomas are not sufficient for advanced research. Therefore, we are establishing several types of sarcomas recapitulating biological characteristics of them including cell lines, organoids, and mouse models in order to develop effective novel treatment against sarcomas.
Methods: In RNAseq, raw data were generated using DNBSEQ-G400. In WES, raw sequence data were generated using Illumina NovaSeq 6000 sequencers.
Participants/Materials: giant cell tumor of bone: 1 case
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000618 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2023/06/29 |
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MOLECULAR DATA
| Participants/Materials |
giant cell tumor of bone (ICD10: C419): 1 case tumor tissue (2nd operation): 1 sample tumor tissue (3rd operation): 1 sample organoid derived xenograft tumor: 1 sample |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000747 |
| Total Data Volume | 69.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
giant cell tumor of bone (ICD10: C419): 1 case normal muscle tissue: 1 sample tumor tissue (2nd operation): 1 sample tumor tissue (3rd operation): 1 sample patient derived organoid: 2 samples organoid derived xenograft tumor: 3 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from normal and tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | MGIEasy RNA Directional Library Prep Set |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000747 |
| Total Data Volume | 69.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toru Wakamatsu
Affiliation: Department of Musculoskeletal Oncology Service, Osaka International Cancer Institute
Project / Group Name: -
URL: https://oici.jp.e.abv.hp.transer.com/hospital/department/gansenmoni/seikei/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Development of sarcoma organoid panel for novel treatment | 20K18048 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic characterization of a novel organoid from human malignant giant-cell tumor | doi: 10.1016/j.jbo.2023.100486 | JGAD000747 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
