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
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000006 | NGS (PBAT) | Controlled Access (Type I) | 2014/12/24 |
| hum0009v1.CpG.v1 | methylation rate at each CpG site | Un-restricted Access | 2015/01/07 |
* Data users need to apply the Form 2 (Application Form 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 Data set ID | JGAD000006 |
| Total Data Volume | 500GB |
| 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
Methylation rate at each CpG site calculated from JGAD000006.
| QC | Bisulfite conversion rates were estimated using reads that uniquely aligned to the lambda phage genome and were >99% for all samples. |
| Mapping Methods | Sequenced reads were processed using the Illumina standard base-calling pipeline (v1.8.2) and the first 4 bases were trimmed to remove random primer sequences. The resulting reads were aligned to the reference genome (UCSC hg19) using Bismark (v.0.9.0) with default parameters. |
| Reference Genome Sequence | UCSC hg19 |
| Coverage（Depth） |
Oocyte-1（amplified）: 4.5 Oocyte-2(not amplified): 2.5 Sperm-1: 7.6 Sperm-2: 8.1 Sperm-3: 8.8 Preimplantation embryos: 23.5 Cord blood cells-1: 3.2 Cord blood cells-2: 3.4 Cord blood cells-3: 3.1 Cord blood cells-4: 3.2 Cord blood cells-5: 3.6 |
| Calculation for Methylation Rate | The methylation level of each cytosine was calculated using the Bismark methylation extractor. For CpG sites, reads from both strands were combined to calculate the methylation levels. |
| Total Reads / Uniquely Mapped Reads |
Oocyte-1: 752 million reads / 144 million reads Oocyte-2: 153 million reads / 80 million reads Sperm-1: 392 million reads / 243 million reads Sperm-2: 457 million reads / 259 million reads Sperm-3: 450 million reads / 281 million reads Preimplantation embryos: 1275 million reads / 750 million reads Cord blood cells-1: 181 million reads / 102 million reads Cord blood cells-2: 185 million reads / 108 million reads Cord blood cells-3: 177 million reads / 98 million reads Cord blood cells-4: 179 million reads / 101million reads Cord blood cells-5: 196 million reads / 114 million reads |
| Data Download |
Methylation rate for preimplantation embryos Methylation rate for cord blood cells-1 |
| Comments (Policies) |
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 |
|---|---|---|
| CREST (Development of Fundamental Technologies for Diagnosis and Therapy Based upon Epigenome Analysis) | Epigenome Analysis of Cells in the Placenta and Endometrium Forming the Fetal-maternal Interface | 107411 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Epigenome Dynamics and Regulation in Germ Cells | 26112502 |
PUBLICATIONS
| Title | DOI | Data Set 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 (Data Set 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 |
