NBDC Research ID: hum0083.v2
SUMMARY
Aims: exploration of biomarkers discriminating squamous cell carcinoma from other lung cancers
Methods: CAGE (Cap Analysis of Gene Expression)
Participants/Materials: 97 + 48 surgically dissected tissues
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000070 | NGS (CAGE-seq) | Controlled-access (Type I) | 2016/10/28 |
| JGAS000488 | NGS (CAGE-seq) | Controlled-access (Type I) | 2022/01/24 |
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MOLECULAR DATA
| Participants/Materials |
lung cancer (ICD10: C34): 97 + 38 cases malignant pleural mesothelioma (ICD10: C450): 10 cases |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNA extracted from surgically dissected tissues |
| Cell Lines | - |
| Library Construction (kit name) | CAGE assay (*References) |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 47 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume | 45 + 30 GB (fastq) |
| Comments (Policies) | NBDC policy |
1) Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung. BMC Cancer 2016; 16:760 (doi: 10.1186/s12885-016-2792-1)
2) Detecting expressed genes using CAGE. Methods Mol Biol. 2014; 1164:67–85. (doi: 10.1007/978-1-4939-0805-9_7)
DATA PROVIDER
Principal Investigator: Yoshihide Hayashizaki / Yasushi Kogo
Affiliation: RIKEN Preventive Medicine and Diagnosis Innovation Program / RIKEN Cluster for Science, Technology and Innovation Hub
Project / Group Name: Genome-wide exploration for biomarkers in thoracic malignant tumors by using CAGE (Kazuya Takamochi, Juntendo University)
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Exploration of biomarkers specific to lung squamous cell carcinoma by using CAGE | 25462185 |
| Smoking Research Foundation | Biomarker exploration and database development for personalized medicine against lung tumor | - |
| Research Grant for RIKEN Omics Science Center from MEXT | - | - |
| Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT | - | - |
| Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), Japan Agency for Medical Research and Development (AMED) | Platform for Drug Discovery, Informatics, and Structural Life Science | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung | doi: 10.1186/s12885-016-2792-1 |
JGAD000070 JGAD000605 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Masafumi Horie | Division for Health Service Promotion, The University of Tokyo | JGAD000070 | 2017/01/11-2021/11/30 |
