NBDC Research ID: hum0009.v3

 

SUMMARY

Aims: To generate single-base resolution DNA methylome maps of human gametes and embryos and uncover DNA methylation dynamics during early human development.

Methods: Whole genome bisulfite sequencing libraries were prepared using the post-bisulfite adaptor tagging (PBAT) method. PBAT libraries were sequenced on the HiSeq 2000 or 2500 platform (Illumina) with 100 bp single-end reads.

Materials: Human oocytes, sperm, preimplantation embryos, and cord blood cells

 

Data Set IDType of DataCriteriaRelease Date
DRA003802 NGS (PBAT) Un-restricted Access 2015/08/03
JGAS00000000006 NGS (PBAT) Controlled Access (Type I) 2014/12/24
hum0009v1.CpG.v1 methylation rate at each CpG site Un-restricted Access 2015/01/07

*Release Note

* The data provider changed the access level of JGAS00000000006 (Controlled Access [Type I]) to Un-restricted Access (DRA003802) from 2015/08/03.

 

MOLECULAR DATA

DRA003802 (Exactly the same data as JGAS00000000006)

Materials

11 samples

Human oocytes, sperm, preimplantation embryos and cord blood cells

(Each DNAs from oocytes and preimplantation embryos were pooled)

Targets PBAT
Target Loci for Capture Methods -
Platform Illumina Hiseq 2000/2500
Library Source

DNAs extracted from each cell

Oocytes (amplified)*1: 79 samples were pooled

Oocytes: 123 samples were pooled

Sperm: 3 samples

Preimplantation embryos: 80 samples were pooled

Cord blood cells: 5 samples

Cell Lines -
Library Construction (kit name) Post-bisulfite Adaptor-tagging (PBAT) method*2
Fragmentation Methods Bisulfite Treatment
Spot Type Single-end Reads
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Data set ID DRA003802
Total Data Volume 500 GB
Comments (Policies)

NBDC policy

*1:Okae, H., et al. (2014) Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development. PLoS Genet. 10(12): e1004868

*2:Miura, F., et al. (2012) Amplification-free Whole Genome Bisulfite Sequencing by Post-bisulfite Adaptor Tagging. Nucleic Acids Res. 40, e136

* When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more

 

JGAS00000000006 (The access level was changed to "Un-restricted Access". Please have a look at DRA003802.)

Materials

11 samples

Human oocytes, sperm, preimplantation embryos and cord blood cells

(Each DNAs from oocytes and preimplantation embryos were pooled)

Targets PBAT
Target Loci for Capture Methods -
Platform Illumina Hiseq 2000/2500
Library Source

DNAs extracted from each cell

Oocytes (amplified)*1: 79 samples were pooled

Oocytes: 123 samples were pooled

Sperm: 3 samples

Preimplantation embryos: 80 samples were pooled

Cord blood cells: 5 samples

Cell Lines -
Library Construction (kit name) Post-bisulfite Adaptor-tagging (PBAT) method*2
Fragmentation Methods Bisulfite Treatment
Spot Type Single-end Reads
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000006
Total Data Volume 500 GB
Comments (Policies) NBDC policy & Company User Limit

*1:Okae, H., et al. (2014) Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development. PLoS Genet. 10(12): e1004868

*2:Miura, F., et al. (2012) Amplification-free Whole Genome Bisulfite Sequencing by Post-bisulfite Adaptor Tagging. Nucleic Acids Res. 40, e136

 

hum0009v1.CpG.v1

Methylation rate at each CpG site was calculated from JGAD00000000006.

QC Bisulfite conversion rates were estimated using reads that uniquely aligned to the lambda phage genome and were >99% for all samples.
Mapping Methods Sequenced reads were processed using the Illumina standard base-calling pipeline (v1.8.2) and the first 4 bases were trimmed to remove random primer sequences. The resulting reads were aligned to the reference genome (UCSC hg19) using Bismark (v.0.9.0) with default parameters.
Reference Genome Sequence UCSC hg19
Coverage (Depth)

Oocyte-1(amplified): 4.5

Oocyte-2(not amplified): 2.5

Sperm-1: 7.6

Sperm-2: 8.1

Sperm-3: 8.8

Preimplantation embryos: 23.5

Cord blood cells-1: 3.2

Cord blood cells-2: 3.4

Cord blood cells-3: 3.1

Cord blood cells-4: 3.2

Cord blood cells-5: 3.6

Calculation for Methylation Rate The methylation level of each cytosine was calculated using the Bismark methylation extractor. For CpG sites, reads from both strands were combined to calculate the methylation levels.
Total Reads / Uniquely Mapped Reads

Oocyte-1: 752 million reads / 144 million reads

Oocyte-2: 153 million reads / 80 million reads

Sperm-1: 392 million reads / 243 million reads

Sperm-2: 457 million reads / 259 million reads

Sperm-3: 450 million reads / 281 million reads

Preimplantation embryos: 1275 million reads / 750 million reads

Cord blood cells-1: 181 million reads / 102 million reads

Cord blood cells-2: 185 million reads / 108 million reads

Cord blood cells-3: 177 million reads / 98 million reads

Cord blood cells-4: 179 million reads / 101million reads

Cord blood cells-5: 196 million reads / 114 million reads

Data Download

Methylation rate for oocyte

Methylation rate for sperm

Methylation rate for preimplantation embryos

Methylation rate for cord blood cells-1

Methylation rate for cord blood cells-2

Hash file

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 / Groupe Name:

Funds / Grants (Research Project Number):

NameTitleProject Number
CREST (Development of Fundamental Technologies for Diagnosis and Therapy Based upon Epigenome Analysis) Epigenome Analysis of Cells in the Placenta and Endometrium Forming the Fetal-maternal Interface 107411
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas Epigenome Dynamics and Regulation in Germ Cells 26112502

 

PUBLICATIONS

TitleDOIData Set ID
1 Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development doi:10.1371/journal.pgen.1004868 DRA003802 (JGAS00000000006)
2