NBDC Research ID: hum0118.v1

 

SUMMARY

Aims: exploration of biomarkers discriminating lymph node metastasis in endometrial cancers

Methods: CAGE (Cap Analysis of Gene Expression), Sanger sequencing

Participants/Materials: surgically dissected tumor tissues from 17 endometrial cancer patients

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000124

NGS (CAGE-seq)

Sanger sequencing

Controlled Access (Type I) 2017/12/11

*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

CAGE-seq

Participants/Materials 15 endometrial cancer patients
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 Data set ID JGAD00000000135
Total Data Volume 5 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)

 

Sanger-seq

Participants/Materials 3 endometrial cancer patients
Targets Sanger sequencing
Target Loci for Capture Methods TACC2(chr10:123,748,689-124,014,057 [ref: hg19])
Platform Thermo Fisher Scientific (ABI) 3500 Genetic Analyzer
Library Source cDNA synthesize from RNA extracted from surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) BigDye Terminator v3.1 Cycle Sequencing kit
Japanese Genotype-phenotype Archive Data set ID JGAD00000000135
Total Data Volume 5 GB (fasta)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Yoshihide Hayashizaki

Affiliation: RIKEN Preventive Medicine and Diagnosis Innovation Program

Project / Group Name:Genome-wide exploration for biomarkers in endometrial cancer by using CAGE (Yasuhisa Terao, Juntendo University)

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (C) Exploration of biomarkers to predict lymph node metastasis in endometrial cancer by using CAGE 15K10732
Research Grant to RIKEN Omics Science Center from MEXT
Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT

 

PUBLICATIONS

TitleDOIData Set ID
1 Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis. doi: 10.1038/s41598-017-14418-5 JGAD00000000135
2

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
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