NBDC Research ID: hum0009.v1
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SUMMARY
Aims: To generate single-base resolution DNA methylome maps of human gametes and embryos and uncover DNA methylation dynamics during early human development.
Methods: Whole genome bisulfite sequencing libraries were prepared using the post-bisulfite adaptor tagging (PBAT) method. PBAT libraries were sequenced on the HiSeq2000 or 2500 platform (Illumina) with 100-bp single-end reads.
Participants/Materials: Human oocytes, sperm, preimplantation embryos, and cord blood cells
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000006 | NGS (PBAT) | Controlled-access (Type I) | 2014/12/24 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
11 samples Human oocytes, sperm, preimplantation embryos and cord blood cells (Each DNAs from oocytes and preimplantation embryos were pooled) |
| Targets | Whole genome bisulphite sequencing |
| Target Loci for Captur Methods | - |
| Platforms | Illumina Hiseq2000/2500 |
| Library Source |
DNAs extracted from each cell Oocytes (amplified)*1: 79 samples were pooled Oocytes: 123 samples were pooled Sperm: 3 samples Preimplantation embryos: 80 samples were pooled Cord blood cells: 5 samples |
| Cell Lines | - |
| Library Construction (kit name) | Post-bisulfite Adaptor-tagging (PBAT) method*2 |
| Fragmentation Methods | Bisulfite Treatment |
| Spot Type | Single-end Reads |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000006 |
| Total Data Volume | 500 GB |
| Comments (Policies) | NBDC policy & Company User Limit |
*1：Okae, H., et al. (2014) Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development. PLoS Genet. 10(12): e1004868
*2：Miura, F., et al. (2012) Amplification-free Whole Genome Bisulfite Sequencing by Post-bisulfite Adaptor Tagging. Nucleic Acids Res. 40, e136
DATA PROVIDER
Principal Investigator: Takahiro Arima
Affiliation: Department of Informative Genetics, Environment and Genome Research Center,Tohoku University Graduate School of Medicine
Project / Groupe Name：
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 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Epigenome Dynamics and Regulation in Germ Cells | 26112502 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development | doi:10.1371/journal.pgen.1004868 | JGAD000006 |
| 2 |
USRES (Controlled-access Data)
| PI | Affiliation | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
| Hidehiro Toh | Medical Institute of Bioregulation Kyushu University | JGAD000006 | 2015/04/08-2018/02/27 |
| David Monk | Bellvitge Institute for Biomedical Research (IDIBELL) | JGAD000006 | 2015/04/13-2016/03/01 |
