NBDC Research ID: hum0090.v1

 

SUMMARY

Aims: The aim of this study is to participate in International Human Epigenome Consortium (http://ihec-epigenomes.org/), through disclosure of quality reference epigenome profiles in normal and diseased cells obtained from multiple Japanese people.

Methods: ChIP-Seq, RNA-seq and PBAT-seq analysis about normal human absorptive epithelial cells purified from colorectal partial resection specimens.

Participants/Materials: Normal human absorptive epithelial cells purified from colorectal partial resection specimens

URL: http://crest-ihec.jp/english/project/index.html

 

Dataset IDType of DataCriteriaRelease Date
JGAS000078 NGS (PBAT-seq) Controlled-access (Type I) 2016/11/18
JGAS000079 NGS (ChIP-seq) Controlled-access (Type I) 2016/11/18
JGAS000080 NGS (RNA-seq) Controlled-access (Type I) 2016/11/18

*Release Note

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

 

MOLECULAR DATA

JGAS000078

Participants/Materials: Normal human absorptive epithelial cells purified from colorectal partial resection specimens : 12
Targets PBAT-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source gDNAs extracted from normal human absorptive epithelial cells purified from colorectal partial resection specimens
Cell Lines -
Library Construction (kit name)

Post-Bisulfite Adaptor-Tagging (PBAT) method

(http://crest-ihec.jp/english/epigenome/index.html)

Fragmentation Methods PBAT method: fragmentation due to bisulfite conversion
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000078
Total Data Volume 1 TB (fastq [61files / 23,164,882,050 reads])
Comments (Policies) NBDC policy

 

JGAS000079

Participants/Materials: Normal human absorptive epithelial cells purified from colorectal partial resection specimens : 12
Targets ChIP-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source gDNAs extracted from normal human absorptive epithelial cells purified from colorectal partial resection specimens
Cell Lines -
Library Construction (kit name)

Anti H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K4me1 and H3K36me3 mouse monoclonal antibodies, kindly provided by Dr. Hiroshi Kimura, Tokyo Institute of Technology, were used for immunoprecipitation.

Fragmentation Methods Ultrasonic fragmentation (BRANSON SLPe, amplitude 40%, on 30 sec and off 30 sec, 10 cycles, on ice)
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 36 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000079
Total Data Volume 171 GB (fastq [85 files / 2,619,042,051 reads])
Comments (Policies) NBDC policy

 

JGAS000080

Participants/Materials: Normal human absorptive epithelial cells purified from colorectal partial resection specimens : 12
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source/span> Total RNA extracted from normal human absorptive epithelial cells purified from colorectal partial resection specimens
Cell Lines -
Library Construction (kit name) Agilent SureSelect Strand Specific RNA kit
Fragmentation Methods Purified poly-A RNA was fragmented with heat treatment and divalent cations.
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000080
Total Data Volume 91 GB (fastq [25 files / 1,189,610,268 reads])
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Yae Kanai

Affiliation: Department of Pathology, Keio University School of Medicine

Project / Group Name: AMED-CREST International Human Epigenome Consortium (IHEC) Team Kanai

URL: http://crest-ihec.jp/english/index.html

URL: http://www.jst.go.jp/kisoken/crest/en/research_area/completed/areah23-4.html

URL: https://pathology.med.keio.ac.jp/home-e/

Funds / Grants (Research Project Number):

Name Title Project Number
Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) Development of Fundamental Technologies for Diagnosis and Therapy Based upon Epigenome Analysis -

 

PUBLICATIONS

Title DOIDataset ID
1
2

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Guillaume Bourque McGill University / McGill University & Genome Quebec Innovation Center

JGAD000078

JGAD000079

JGAD000080

2018/06/07-2020/03/20
Martin Hirst BC Cancer

JGAD000078

JGAD000079

JGAD000080

2018/08/06-2022/05/31
Anton Wellstein Georgetown University School of Medicine, Department of Oncology Biomarkers to evaluate immune related adverse events (irAEs) due to treatment with immune checkpoint inhibitors (ICIs) JGAD000078 2020/11/06-2021/09/01
Michiaki Hamada Faculty of Science and Engineering, Waseda University Japan Construction of RNA-targeted Drug Discovery Database JGAD000080 2022/12/26-2025/03/31