NBDC Research ID: hum0086.v2
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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 [CT], syncytiotrophoblast [ST], extravillous trophoblast [EVT], trophoblast stem cells [TS] derived from CT, ST differentiated from TS, EVT differentiated from TS, stroma), uterus (endometrium epithelial, stroma)
URL： http://crest-ihec.jp/english/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000073 JGAS000107 |
Controlled-access (Type I) |
2017/09/25 2017/12/26 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma): 20 samples + 4 samples (female TS, ST from TS, and EVT from TS / male TS) |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500/2500] |
| Library Source | DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), or trophoblast stem cells |
| 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 | |
| Total Data Volume | About 2,405 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma): 20 samples + 4 samples (female TS, ST from TS, EVT from TS, and placental stroma) |
| Targets | ChIP-seq |
| Target Loci for Capture Methods |
antibodies: H3K4me3、H3K4me1、H3K9me3、H3K27ac、H3K27me3、H3K36me3 Input |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma), uterus (endometrium epithelial, stroma), trophoblast stem cells |
| Cell Lines | - |
| Library Construction (kit name) | Ovation Ultralow System V2 kit 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 | |
| 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 + 6 samples (female TS, ST from TS, EVT from TS / male TS, ST from TS, EVT from TS) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | mRNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), or trophoblast stem cells |
| 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 | |
| Total Data Volume | About 432 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma): 19 samples + 3 samples (female TS, ST from TS, and EVT from TS) |
| Targets | small RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500/2500] |
| Library Source | RNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), or trophoblast stem cells |
| 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 | |
| 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) |
| 3 | Derivation of Human Trophoblast Stem Cells | doi: 10.1016/j.stem.2017.11.004 | JGAD000115 |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
| Nehemiah Alvarez | De Novo Genomics Corporation |
JGAD000073 JGAD000115 |
2018/02/02-2018/12/31 |
| R. Michael Roberts | University of Missouri, Animal Sciences / Biochemistry |
JGAD000073 JGAD000115 |
2018/03/02-2019/02/15 |
| Guillaume Bourque | McGill University / McGill University & Genome Quebec Innovation Center |
JGAD000073 JGAD000115 |
2018/06/07-2019/03/22 |
