NBDC Research ID: hum0112.v1
SUMMARY
Aims: To establish human trophoblast stem cells from blastocyst, and to characterize them.
Methods: PBAT-seq, ChIP-seq, RNA-seq, and miRNA-seq
Participants/Materials: trophoblast stem cell (TS)
URL: http://ihec-epigenomes.org/ (The processed data will soon be released on the IHEC Data Portal)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000112 (JGA000122) |
Controlled-access (Type I) | 2017/12/14 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials: | trophoblast stem cell: 3 samples (1 TS, 3 culture conditions) |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500] |
| Library Source | DNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | Post-Bisulfite Adaptor-Tagging (PBAT) |
| Fragmentation Methods | PBAT method: fragmentation due to bisulfite conversion |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | trophoblast stem cell: 18 samples (TS: 1, 3 culture conditions, 6 antibodies [anti H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3 antibodies]) + 1 negative control |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | Ovation Ultralow System V2 kit (NuGEN) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris M220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | trophoblast stem cell: 6 samples (2 TSs, 3 culture conditions) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | mRNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | trophoblast stem cell: 3 samples (1 TS, 3 culture conditions) |
| Targets | miRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500] |
| Library Source | RNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 64 or 68 bp (including adaptor) bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takahiro Arima
Affiliation: Department of Informative Genetics, Environment and Genome Research Center,Tohoku University Graduate School of Medicine
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, http://ihec-epigenomes.org/
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) | Epigenome analysis of cells in the placenta and endometrium forming the fetal-maternal interface | JP17gm0510011 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Derivation of Human Trophoblast Stem Cells | doi: 10.1016/j.stem.2017.11.004 |
JGAD000121 JGAD000115 (hum0086) |
| 2 |
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 | JGAD000121 | 2018/01/15-2018/12/31 | ||
| R. Michael Roberts | University of Missouri, Animal Sciences / Biochemistry | JGAD000121 | 2018/03/02-2019/02/15 | ||
| Zhigang Xue | School of Medicine and Life Science, Tongji University | JGAD000121 | 2018/12/17-2022/12/31 | ||
| Todd Macfarlan | National Institute of Child Health and Human Development | JGAD000121 | 2018/12/17-2019/10/31 | ||
| Howard Fine | Weill Cornell Medicine | JGAD000121 | 2018/12/18-2023/12/10 | ||
| William S.B. Yeung | Department of Obstetrics and Gynaecology, the University of Hong Kong | JGAD000121 | 2019/02/12-2020/12/13 | ||
| 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 | JGAD000121 | 2020/01/15-2023/12/30 | |
| Thorold W. Theunissen | Washington University School of Medicine in St. Louis | Assessment of trophoblast fates derived from human pluripotent stem cells | JGAD000121 | 2020/01/22-2021/09/16 | |
| Lin GAO | The Hong Kong University of Science and Technology | Defining the transcriptional regulatory roles of retrotransposons in human placenta cells. | JGAD000121 | 2021/08/11-2024/05/28 | |
| 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 | JGAD000121 | 2022/04/20-2023/03/31 |
| Ming-an Sun | Yangzhou University College of Veterinary Medicine | China | The activation and function of endogenous retroviruses in mammalian placentae | JGAD000121 | 2022/06/20-2024/06/30 |
| Xinzhi Zhao | International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University | China | Research on epigenetic regulations of placenta-specific enhancers associated with preeclampsia. | JGAD000121 | 2022/12/09-2023/10/19 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000121 | 2022/12/26-2025/03/31 |
| Paul Robson | The Jackson Laboratory for Genomic Medicine | United States of America | Modeling extra-embryonic mesoderm lineage development with human induced pluripotent stem cells | JGAD000121 | 2024/02/09-2026/12/26 |
