NBDC Research ID: hum0083.v1

 

SUMMARY

Aims: exploration of biomarkers discriminating squamous cell carcinoma from other lung cancers

Methods: CAGE (Cap Analysis of Gene Expression)

Participants/Materials: 97 surgically dissected tissues

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000070 NGS (CAGE-seq) Controlled Access (Type I) 2016/10/28

*Release Note 

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000070

Participants/Materials 97 lung cancer patients
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 Data set ID JGAD00000000070
Total Data Volume 45 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

Affiliation: RIKEN Preventive Medicine and Diagnosis Innovation Program

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 - -

 

PUBLICATIONS

TitleDOIData Set 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 JGAD00000000070
2

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Masafumi Horie ​Division for Health Service Promotion, The University of Tokyo JGAD00000000070 2017/01/11-2021/11/30