NBDC Research ID: hum0086.v3

 

SUMMARY

Aims: As a member of the International Human Epigenome Consortium (IHEC), we obtain high-quality standard epigenome profiles of placenta tissue from Japanese donors, and open the data to public to promote basic research in human epigenome.

Methods: PBAT-seq, ChIP-seq, RNA-seq, and small RNA-seq

Participants/Materials: placenta (cytotrophoblast [normal/CT, fetal growth restriction/FGR-CT, preeclampsia/PE-CT, trisomy 18/Tri-18-CT], syncytiotrophoblast [ST], extravillous trophoblast [EVT], trophoblast stem cells [TS] derived from female/male CT, ST differentiated from TS, EVT differentiated from TS, stroma), uterus (endometrium epithelial, stroma), hydatidiform mole

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

 

Dataset IDType of DataCriteriaRelease Date

JGAS000073
(JGA000074)

JGAS000107
(JGA000117)

NGS (PBAT-seq)

NGS (ChIP-seq)

NGS (RNA-seq)

NGS (small RNA-seq)

Controlled-access (Type I)

2017/09/25

2017/12/26

2018/06/26

*Release Note

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

 

MOLECULAR DATA

PBAT-seq

Participants/Materials: placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), hydatidiform mole (ICD10: O010), female TS, ST from TS and EVT from TS / male TS: total 28 samples
Targets PBAT-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 1500/2500]
Library Source DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), hydatidiform mole, or trophoblast stem cells
Cell Lines -
Library Construction (kit name) Post-Bisulfite Adaptor-Tagging (PBAT) method
Fragmentation Methods PBAT method: fragmentation due to bisulfite conversion
Spot Type Paired-end / Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 101 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000073

JGAD000115

Total Data Volume

JGAD000073: 4.08 TB (fastq)

JGAD000115: 339.44 GB (fastq)

Comments (Policies) NBDC policy

 

ChIP-seq

Participants/Materials: placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma), female TS, ST from TS, EVT from TS: total 25 samples
Targets ChIP-seq
Target Loci for Capture Methods

antibodies: H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3

Input

Platform Illumina [HiSeq 2500]
Library Source DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma), uterus (endometrium epithelial, stroma), trophoblast stem cells
Cell Lines -
Library Construction (kit name) Ovation Ultralow System V2 kit (NuGEN) and NEBNext UltraII DNA Library Prep Kit for Illumina
Fragmentation Methods Ultrasonic fragmentation (Covaris M220)
Spot Type Paired-end / Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 51 - 126 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000073

JGAD000115

Total Data Volume

JGAD000073: 4.08 TB (fastq)

JGAD000115: 339.44 GB (fastq)

Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials: placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma), female TS, ST from TS, EVT from TS / male TS, ST from TS, EVT from TS: total 34 samples
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source mRNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma), uterus (endometrium epithelial, stroma), or trophoblast stem cells
Cell Lines -
Library Construction (kit name) TruSeq Stranded mRNA LT Sample Prep Kit
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 101 - 126 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000073

JGAD000115

Total Data Volume

JGAD000073: 4.08 TB (fastq)

JGAD000115: 339.44 GB (fastq)

Comments (Policies) NBDC policy

 

small RNA-seq

Participants/Materials: placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma), female TS, ST from TS, and EVT from TS: total 23 samples
Targets small RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 1500/2500]
Library Source RNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), or trophoblast stem cells
Cell Lines -
Library Construction (kit name) NEBNext Small RNA Library Prep Set for Illumina
Fragmentation Methods -
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 64/68 bp (including adaptor)
Japanese Genotype-phenotype Archive Dataset ID

JGAD000073

JGAD000115

Total Data Volume

JGAD000073: 4.08 TB (fastq)

JGAD000115: 339.44 GB (fastq)

Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Hiroyuki Sasaki

Affiliation: Medical Institute of Bioregulation, Kyushu University

Project / Group Name: Core Research and Evolutional Science and Technology (CREST), International Human Epigenome Consortium (IHEC), Sasaki Team

URL: http://crest-ihec.jp/english/index.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 DOIDataset ID
1 The International Human Epigenome Consortium: A blueprint for scientific collaboration and discovery. doi: 10.1016/j.cell.2016.11.007 JGAD000073
2 Allele-specific methylome and transcriptome analysis reveals widespread imprinting in the human placenta doi: 10.1016/j.ajhg.2016.08.021 JGAD000038 (hum0040)
3 Derivation of Human Trophoblast Stem Cells doi: 10.1016/j.stem.2017.11.004

JGAD000115

JGAD000121 (hum0112)

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Nehemiah Alvarez De Novo Genomics Corporation JGAD000073,
JGAD000115
2018/02/02-2018/12/31
R. Michael Roberts University of Missouri, Animal Sciences / Biochemistry JGAD000073,
JGAD000115
2018/03/02-2019/02/15
Guillaume Bourque McGill University / McGill University & Genome Quebec Innovation Center JGAD000073,
JGAD000115
2018/06/07-2020/03/20
Martin Hirst BC Cancer JGAD000073,
JGAD000115
2018/08/06-2022/05/31
Zhaobo Lin ShanghaiTech University JGAD000073,
JGAD000115
2018/11/12-2020/09/01
Zhigang Xue School of Medicine and Life Science, Tongji University JGAD000073,
JGAD000115
2018/12/17-2022/12/31
Todd Macfarlan National Institute of Child Health and Human Development JGAD000073,
JGAD000115
2018/12/17-2019/10/31
William S.B. Yeung Department of Obstetrics and Gynaecology, the University of Hong Kong JGAD000073,
JGAD000115
2019/02/12-2020/12/13
Amir Eden Department of Cell and Developmental Biology, Insitute of Life Sciences, The Hebrew University of Jerusalem JGAD000073,
JGAD000115
2019/05/07-2021/09/30
Austin Smith Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge Comparison of trophoblast stem cell cultures JGAD000073,
JGAD000115
2019/08/19-2021/10/31
Thorold W. Theunissen Washington University School of Medicine in St. Louis Assessment of trophoblast fates derived from human pluripotent stem cells JGAD000073,
JGAD000115
2019/12/06-2021/09/16
Hui Li Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine Derivation of Human Induced Trophoblast Stem Cells from Embryonic Stem Cells JGAD000073,
JGAD000115
2020/01/15-2023/12/30
Masatoshi Ohgushi Lab. of Developmental System, Instutute for Frontier Life and Medical Sciences, Kyoto University Exploring differentiaton potential of human pluripotent stem cells JGAD000073,
JGAD000115
2020/03/19-2022/09/26
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) JGAD000073,
JGAD000115
2020/11/06-2021/09/01
Kichoon Lee Department of Animal Sciences, The Ohio State University Investigation on allele-specific gene expressions in humans JGAD000073,
JGAD000115
2021/05/24-2021/12/31
Kenichiro Hata Maternal fetal biology, National Research Institute for Child Health and Development Genetic and genomic analysis of fetal developmental abnormalities JGAD000073,
JGAD000115
2021/06/11-2022/03/31
Lin GAO The Hong Kong University of Science and Technology Defining the transcriptional regulatory roles of retrotransposons in human placenta cells. JGAD000073,
JGAD000115
2021/08/11-2024/05/28
Kenichiro Hata Maternal fetal biology, National Research Institute for Child Health and Development Genetic and genomic analysis of fetal developmental abnormalities JGAD000073,
JGAD000115
2022/01/05-2022/03/31
Gianluca Ursini Lieber Institute for Brain Development, Johns Hopkins University School of Medicine United States of America Analysis of the transcriptional profile of Human Trophoblast Stem Cells JGAD000073,
JGAD000115
2022/04/20-2023/03/31
Michiaki Hamada Faculty of Science and Engineering, Waseda University Japan Construction of RNA-targeted Drug Discovery Database JGAD000073,
JGAD000115
2022/12/26-2025/03/31
Wilfried Haerty Earlham Institute United Kingdom of Great Britain and Northern Ireland Understanding epigenetic drift in a transient reproductive tissue - defining the effects on gestation ageing and cell identity within the placenta JGAD000073,
JGAD000115
2023/04/10-2024/01/31
Paul Robson The Jackson Laboratory for Genomic Medicine United States of America Modeling extra-embryonic mesoderm lineage development with human induced pluripotent stem cells JGAD000073,
JGAD000115
2024/02/09-2026/12/26
Masatsugu Ema Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science Japan Isolation and characterization of trophoblast stem cells from human placenta JGAD000073,
JGAD000115
2024/08/19-2026/08/31