NBDC Research ID: hum0086.v1
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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: Whole Genome Biosulfite Sequencing (WGBS), ChIP-seq, RNA-seq, and small RNA-seq
Participants/Materials: placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma)
URL: http://crest-ihec.jp/english/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000073 | Controlled-access (Type I) | 2017/09/25 |
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MOLECULAR DATA
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma): 20 samples |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500/2500] |
| Library Source | DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) or uterus (endometrium epithelial, stroma) |
| 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 | JGAD000073 |
| Total Data Volume | About 2,405 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma): 20 samples |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) or uterus (endometrium epithelial, stroma) |
| 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 | JGAD000073 |
| Total Data Volume | About 1,383 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma): 20 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | mRNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) or uterus (endometrium epithelial, stroma) |
| 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 | JGAD000073 |
| Total Data Volume | About 432 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma): 19 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) or uterus (endometrium epithelial, stroma) |
| 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 | JGAD000073 |
| Total Data Volume | About 14 GB |
| 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, 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) |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
