NBDC Research ID: hum0086.v3

 

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 [normal/CT, fetal growth restriction/FGR-CT, preeclampsia/PE-CT, trisomy 18/Tri-18-CT], syncytiotrophoblast [ST], extravillous trophoblast [EVT], trophoblast stem cells [TS] derived from female/male CT, ST differentiated from TS, EVT differentiated from TS, stroma), uterus (endometrium epithelial, stroma), hydatidiform mole

URL: http://crest-ihec.jp/english/index.html

 

Data Set IDType of DataCriteriaRelease Date

JGAS00000000073
(JGA00000000074)

JGAS00000000107
(JGA00000000117)

NGS (WGBS)

NGS (ChIP-seq)

NGS (RNA-seq)

NGS (small RNA-seq)

Controlled Access (Type I)

2017/09/25

2017/12/26

2018/06/26

*Release Note  

* 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

NGS (WGBS)

Participants/Materials: placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), hydatidiform mole (ICD10: O010), female TS, ST from TS and EVT from TS / male TS: total 28 samples
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), hydatidiform mole, 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 Data set ID

JGAD00000000073

JGAD00000000115

Total Data Volume About 2,537 GB
Comments (Policies) NBDC policy

 

NGS (ChIP-seq)

Participants/Materials: placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma), female TS, ST from TS, EVT from TS: total 25 samples
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 (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 Data set ID

JGAD00000000073

JGAD00000000115

Total Data Volume About 1,488 GB
Comments (Policies) NBDC policy

 

NGS (RNA-seq)

Participants/Materials: placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma), female TS, ST from TS, EVT from TS / male TS, ST from TS, EVT from TS: total 34 samples
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source mRNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma), uterus (endometrium epithelial, stroma), or trophoblast stem cells
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 - 126 bp
Japanese Genotype-phenotype Archive Data set ID

JGAD00000000073

JGAD00000000115

Total Data Volume About 564 GB
Comments (Policies) NBDC policy

 

NGS (small RNA-seq)

Participants/Materials: placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma), female TS, ST from TS, and EVT from TS: total 23 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), uterus (endometrium epithelial, stroma), or trophoblast stem cells
Cell Lines -
Library Construction (kit name) NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs)
Fragmentation Methods -
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 64/68 bp (including adaptor)
Japanese Genotype-phenotype Archive Data set ID

JGAD00000000073

JGAD00000000115

Total Data Volume About 16 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, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) Development of Fundamental Technologies for Diagnosis and Therapy Based upon Epigenome Analysis

 

PUBLICATIONS

Title DOIData Set ID
1 The International Human Epigenome Consortium: A blueprint for scientific collaboration and discovery. doi: 10.1016/j.cell.2016.11.007 JGAD00000000073
2 Allele-specific methylome and transcriptome analysis reveals widespread imprinting in the human placenta doi: 10.1016/j.ajhg.2016.08.021 JGAD00000000038 (hum0040)
3 Derivation of Human Trophoblast Stem Cells doi: 10.1016/j.stem.2017.11.004 JGAD00000000115

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Nehemiah Alvarez De Novo Genomics Corporation

JGAD00000000073

JGAD00000000115

2018/02/02-2018/12/31
R. Michael Roberts University of Missouri, Animal Sciences / Biochemistry

JGAD00000000073

JGAD00000000115

2018/03/02-2019/02/15
Guillaume Bourque McGill University / McGill University & Genome Quebec Innovation Center

JGAD00000000073

JGAD00000000115

2018/06/07-2019/03/22
Martin Hirst BC Cancer

JGAD00000000073

JGAD00000000115

2018/08/06-2022/05/31
Zhaobo Lin ShanghaiTech University

JGAD00000000073

JGAD00000000115

2018/11/12-2020/09/01
Zhigang Xue School of Medicine and Life Science, Tongji University

JGAD00000000073

JGAD00000000115

2018/12/17-2022/12/31
Todd Macfarlan National Institute of Child Health and Human Development

JGAD00000000073

JGAD00000000115

2018/12/17-2019/10/31