NBDC Research ID: hum0536.v1
SUMMARY
Aims: Malignant pleural mesothelioma is an aggressive pleural tumor with poor prognosis. Understanding the molecular mechanisms underlying its development and progression is essential for improving diagnosis and treatment. This study aims to identify clinically relevant molecular pathways through genomic and transcriptome analyses of tumor and non-tumor pleural tissues. Candidate genes associated with tumor initiation and progression will be analyzed in terms of gene expression, localization, dynamics, and cell-to-cell interactions. Their correlation with clinicopathological parameters will also be investigated. Tumor tissues will be preserved by cryopreservation or transplantation into immunodeficient mice to enable further studies using in vivo models or in vitro cell culture systems.
Methods: WGS, single-cell RNA-seq, ATAC-seq
Participants/Materials: One pleural mesothelioma patient
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000859 | NGS (WGS, scRNA-seq, ATAC-seq) | Controlled-access (Type I) | 2026/04/08 |
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MOLECULAR DATA
| Participants/Materials: |
Pleural mesothelioma (ICD10: C45.0): 1 case tumor tissues: 2 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Illumina DNA PCR-Free Prep Kit |
| Fragmentation Methods | Transposome-mediated on-bead tagmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001002 |
| Total Data Volume | 680.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
Pleural mesothelioma (ICD10: C45.0): 1 case tumor tissue: 1 sample Patient-derived xenograft (PDX) tumor model specimen: 2 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from enzymatically dissociated tumor samples |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 5' Reagent Kits v2 Dual Index, Library Construction Kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | Read1: 26 bp, Read2: 90bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001002 |
| Total Data Volume | 680.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
Pleural mesothelioma (ICD10: C45.0): 1 case Patient-derived cell line: 2 samples |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from cell line |
| Cell Lines | - |
| Library Construction (kit name) | ATAC-Seq Kit（Active Motif） |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001002 |
| Total Data Volume | 680.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shumpei Ishikawa
Affiliation: Department of Preventive Medicine, 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 (S) | A New Definition of Heterogeneity in Gastric Cancer through Quantitative Integration of Spatial Tissue and Genomic Information | 22H04990 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Trajectory Analysis of Genomic and Pathological Information during the Treatment Course of Refractory Cancers | JP24ck0106904 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of a Novel Neutrophil–Tumor Interaction in Diffuse-Type Gastric Cancer | 23K27436 |
| KAKENHI Grant-in-Aid for JSPS Fellows | Mechanistic Dissection of Tumor–Stromal Interactions and Identification of Therapeutic Targets in Malignant Pleural Mesothelioma | 23KJ0836 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Cooperative Response Loops Enhanced by Histamine Signaling during Tumor-Neutrophil Crosstalk in Pleural Mesothelioma | JGAD001002 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
