NBDC Research ID: hum0323.v1

 

SUMMARY

Aims: Exploration of biomarkers for early diagnosis and prognosis of colon cancer.

Methods: RNA extracts of colon cancer tissues dissected by surgery are subjected to CAGE profiling.

Participants/Materials: 45 colon cancers

 

Dataset IDType of DataCriteriaRelease Date
JGAS000489 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

JGAS000489

Participants/Materials colon cancer (ICD10: C18.9): 45 cases
Targets CAGE-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNA extracted from surgically dissected tumor 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 JGAD000606
Total Data Volume 19.2 GB (fastq)
Comments (Policies) NBDC policy

*References for CAGE assay

1) 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: Yasushi Kogo

Affiliation: RIKEN Cluster for Science, Technology and Innovation Hub

Project / Group Name:Genome-wide exploration for diagnostic biomarkers in colon cancer by using CAGE (Kazuhiro Sakamoto, Kiichi Sugimoto at Juntendo University; Yoshihide Hayashizaki at RIKEN Preventive Medicine & Diagnosis Innovation Program)

Funds / Grants (Research Project Number):

NameTitleProject Number
Research Grant to RIKEN Omics Science Center from MEXT - -
Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT - -

 

PUBLICATIONS

TitleDOIDataset ID
1
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use