NBDC Research ID: hum0009.v3
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 HiSeq 2000 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 |
|---|---|---|---|
| DRA003802 | NGS (PBAT-seq) | Unrestricted-access | 2015/08/03 |
| JGAS000006 | NGS (PBAT-seq) | Controlled-access (Type I) | 2014/12/24 |
| hum0009v1.CpG.v1 | methylation rate at each CpG site | Unrestricted-access | 2015/01/07 |
* When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
* The data provider changed the access level of JGAS000006 (Controlled-access [Type I]) to Unrestricted-access (DRA003802) from 2015/08/03.
MOLECULAR DATA
DRA003802 (Exactly the same data as JGAS000006)
| Materials |
11 samples Human oocytes, sperm, preimplantation embryos and cord blood cells (Each DNAs from oocytes and preimplantation embryos were pooled) |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| 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 |
| DDBJ Sequence Read Archive ID | DRA003802 |
| Total Data Volume | 500 GB |
| Comments (Policies) |
*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
JGAS000006 （The access level was changed to "Unrestricted-access". Please have a look at DRA003802.)
| Materials |
11 samples Human oocytes, sperm, preimplantation embryos and cord blood cells (Each DNAs from oocytes and preimplantation embryos were pooled) |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| 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
Methylation rate at each CpG site was 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 |
|---|---|---|
| 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 | DRA003802 (JGAS000006) |
| 2 |
