NBDC Research ID: hum0040.v1
SUMMARY
Aims: Genome-wide identification of parent-of-origin dependent DNA methylation and gene expression in the human placenta
Methods: SNPs in human placentas and maternal blood cells were identified using Whole-Genome or Exome sequencing. Allele-specific DNA methylation and gene expression analyses were performed using the human placentas.
Participants/Materials: Human placentas and maternal blood samples
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000038 | Controlled-access (Type I) | 2016/09/16 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
2 human placentas 2 maternal blood samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | gDNAs extracted from human placentas and maternal blood cells |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA LT Sample Prep Kit (Illumina) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris M220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000038 |
| Total Data Volume | About 540 GB (fastq.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
24 human placentas 24 maternal blood samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | gDNAs extracted from human placentas and maternal blood cells |
| Cell Lines | - |
| Library Construction (kit name) |
SureSelect Human All Exon V5+UTRs Kit (Agilent) TruSeq Nano DNA LT Sample Prep Kit (Illumina) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris M220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000038 |
| Total Data Volume | About 490 GB (fastq.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 15 human placentas |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | gDNAs extracted from human placentas |
| Cell Lines | - |
| Library Construction (kit name) | PBAT or NEBNext Ultra DNA Library Prep Kit |
| Fragmentation Methods |
Ultrasonic fragmentation (Covaris M220) No fragmentation for PBAT |
| Spot Type | Paired-end or Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000038 |
| Total Data Volume | About 320 GB (fastq.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 21 human placentas |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from human placentas |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) |
| Fragmentation Methods | Heat Treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000038 |
| Total Data Volume | About 220 GB (fastq.gz) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takahiro Arima
Affiliation: Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine
Project / Group Name: Epigenome Analysis of Cells in the Placenta and Endometrium Forming the Fetal-maternal Interface
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 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Allele-specific methylome and transcriptome analysis reveals widespread imprinting in the human placenta | doi: 10.1016/j.ajhg.2016.08.021 | JGAD000038 |
| 2 | Derivation of Human Trophoblast Stem Cells | doi: 10.1016/j.stem.2017.11.004 | JGAD000038 JGAX000007522 JGAX000007532 JGAX000007538 JGAX000007488 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Martin Hirst | BC Cancer | JGAD000038 | 2018/08/06-2022/05/31 | ||
| Zhigang Xue | School of Medicine and Life Science, Tongji University | JGAD000038 | 2018/12/17-2022/12/31 | ||
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000038 | 2022/12/26-2025/03/31 |
| Masatsugu Ema | Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science | Japan | Isolation and characterization of trophoblast stem cells from human placenta | JGAD000038 | 2024/08/19-2026/08/31 |
