NBDC Research ID: hum0032.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 WGBS analysis about normal and diseased human hepatocytes purified from partial hepatectomy specimens.

Participants/Materials: Normal and diseased human hepatocytes purified from partial hepatectomy specimens (normal human hepatocytes: 6, hepatitis B virus (HBV)-positive human hepatocyte 1 and hepatitis C virus (HCV)-positive human hepatocyte 1.

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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000026 NGS (WGBS) Controlled Access (Type I) 2016/07/22
JGAS00000000027 NGS (ChIP-seq) Controlled Access (Type I) 2016/07/22
JGAS00000000028 NGS (RNA-seq) Controlled Access (Type I) 2016/07/22

*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

JGAS00000000026

Participants/Materials:

Normal and diseased human hepatocytes purified from partial hepatectomy specimens

- Normal human hepatocytes: 6

- HBV-positive human hepatocyte 1: 1

- HCV-positive human hepatocyte 1: 1

Targets WGBS
Target Loci for Capture Methods

-

Platform Illumina [HiSeq 2000]
Library Source gDNAs extracted from normal and diseased human hepatocytes purified from partial hepatectomy 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 Data set ID JGAD00000000026
Total Data Volume 76 GB (fastq [8664 files / 16,901,103,593 reads])
Comments (Policies) NBDC policy

 

JGAS00000000027

Participants/Materials:

Normal and diseased human hepatocytes purified from partial hepatectomy specimens

- Normal human hepatocytes: 6

- HBV-positive human hepatocyte 1: 1

- HCV-positive human hepatocyte 1: 1

Targets ChIP-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source gDNAs extracted from normal and diseased human hepatocytes purified from partial hepatectomy 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 Data set ID JGAD00000000027
Total Data Volume 90 GB (fastq [601 files / 2,299,849 reads])
Comments (Policies) NBDC policy

 

JGAS00000000028

Participants/Materials:

Normal and diseased human hepatocytes purified from partial hepatectomy specimens

- Normal human hepatocytes: 6

- HBV-positive human hepatocyte 1: 1

- HCV-positive human hepatocyte 1: 1

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source/span> Total RNA extracted from normal and diseased human hepatocytes purified from partial hepatectomy specimens.
Cell Lines -
Library Construction (kit name)

TruSeq RNA Library Preparation Kit v2 (Illumina)

SureSelect Strand Specific RNA kit (Agilent)

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 Data set ID JGAD00000000028
Total Data Volume 76 GB (fastq [644 files / 1,092,677,168 reads])
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Yae Kanai

Affiliation: Division of Molecular Pathology, National Cancer Center Research Institute

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: http://www.nccri.ncc.go.jp/en/divisions/01pathology/01path02.html

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 DOIData Set ID
1 Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. doi: 10.1093/nar/gks454 JGAD00000000026
2 Multilayer-omics analyses of human cancers: exploration of biomarkers and drug targets based on the activities of the International Human Epigenome Consortium. doi: 10.3389/fgene.2014.00024 -

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Guillaume Bourque McGill University / McGill University & Genome Quebec Innovation Center

JGAD00000000026

JGAD00000000027

JGAD00000000028

2018/06/07-2019/03/22
Martin Hirst BC Cancer

JGAD00000000026

JGAD00000000027

JGAD00000000028

2018/08/06-2022/05/31