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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000038

Whole Genome Sequencing (WGS)

Whole Exon sequencing (WES)

Bisulfite sequencing (BS-seq)

RNA-seq

Controlled Access (Type I) 2016/09/16

*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

Whole Genome Sequencing

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 Data set ID JGAD00000000038
Total Data Volume About 540 GB (fastq.gz)
Comments (Policies) NBDC policy

 

Whole Exon sequencing

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 Data set ID JGAD00000000038
Total Data Volume About 490 GB (fastq.gz)
Comments (Policies) NBDC policy

 

Bisulfite sequencing

Participants/Materials 15 human placentas
Targets BS-seq
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 Data set ID JGAD00000000038
Total Data Volume About 320 GB (fastq.gz)
Comments (Policies) NBDC policy

 

RNA-seq

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 Data set ID JGAD00000000038
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) Epigenomic analysis of the human placenta and endometrium constituting the fetal-maternal interface 17gm0510011h0006

 

PUBLICATIONS

TitleDOIData Set ID
1 Allele-specific methylome and transcriptome analysis reveals widespread imprinting in the human placenta doi: 10.1016/j.ajhg.2016.08.021 JGAD00000000038
2 Derivation of Human Trophoblast Stem Cells doi: 10.1016/j.stem.2017.11.004 JGAD00000000038
JGAX00000007522
JGAX00000007532
JGAX00000007538
JGAX00000007488

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Martin Hirst BC Cancer JGAD00000000038 2018/08/06-2022/05/31
Zhigang Xue School of Medicine and Life Science, Tongji University JGAD00000000038 2018/12/17-2022/12/31