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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000073 JGAS000107 |
Controlled-access (Type I) |
2017/09/25 2017/12/26 2018/06/26 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| 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 | |
| Total Data Volume |
JGAD000073: 4.08 TB (fastq) JGAD000115: 339.44 GB (fastq) |
| Comments (Policies) | NBDC policy |
| 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 | |
| Total Data Volume |
JGAD000073: 4.08 TB (fastq) JGAD000115: 339.44 GB (fastq) |
| Comments (Policies) | NBDC policy |
| 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 | |
| Total Data Volume |
JGAD000073: 4.08 TB (fastq) JGAD000115: 339.44 GB (fastq) |
| Comments (Policies) | NBDC policy |
| 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 | |
| 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 | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data 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 |
