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 IDType of DataCriteriaRelease Date
JGAS000070 NGS (CAGE-seq) Controlled-access (Type I) 2016/10/28
JGAS000488 NGS (CAGE-seq) Controlled-access (Type I) 2022/01/24

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

JGAS000070 / JGAS000488

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

JGAD000070

JGAD000605

Total Data Volume 45 + 30 GB (fastq)
Comments (Policies) NBDC policy

*References for CAGE assay

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationResearch TitleData 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