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 PBAT-seq 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
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000026 | NGS (PBAT-seq) | Controlled-access (Type I) | 2016/07/22 |
| JGAS000027 | NGS (ChIP-seq) | Controlled-access (Type I) | 2016/07/22 |
| JGAS000028 | NGS (RNA-seq) | Controlled-access (Type I) | 2016/07/22 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| 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 | PBAT-seq |
| 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 |
| 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 | JGAD000026 |
| Total Data Volume | 76 GB (fastq [8664 files / 16,901,103,593 reads]) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID | JGAD000027 |
| Total Data Volume | 90 GB (fastq [601 files / 2,299,849 reads]) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID | JGAD000028 |
| Total Data Volume | 76 GB (fastq [644 files / 1,092,677,168 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 | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. | doi: 10.1093/nar/gks454 | JGAD000026 |
| 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 | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Guillaume Bourque | McGill University / McGill University & Genome Quebec Innovation Center |
JGAD000026 JGAD000027 JGAD000028 |
2018/06/07-2020/03/20 | ||
| Martin Hirst | BC Cancer |
JGAD000026 JGAD000027 JGAD000028 |
2018/08/06-2022/05/31 | ||
| Quan Long | University of Calgary, Faculty of Medicine, Department of Biochemistry & Molecular Biology |
JGAD000026 JGAD000027 JGAD000028 |
2019/01/21-2023/08/31 | ||
| 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) | JGAD000026 | 2020/11/06-2021/09/01 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000028 | 2022/12/26-2025/03/31 |
