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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

NHA000004

Type of data
methylation rate at each CpG site
Access criteria
Unrestricted-access
Total data volume
1.8 GB
File formats
  • TXT
  • ZIP
Research
hum0009
Date published
2015-01-07
Date modified
2015-01-07
Secondary ID
hum0009.v1.CpG.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Blastocyst.zip209 MB
Blood-1.zip469 MB
Blood-2.zip299 MB
Hash.txt910 B
Oocyte.zip275 MB
Sperm.zip541 MB

Analysis method

PBAT-seq (DNA メチル化解析)

Materials and participants
  • Health status
    Healthy
  • Subject count
    11 (Sample)
  • Sex
    Mixed
  • Age group
    Mixed
Sample description
  • Tissue
    Cord blood, Embryo, Oocyte, Sperm
  • Tumor / normal
    Normal
Experimental method
Methyl-seq
Reference genome
GRCh37
Mapping
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.
QC and filtering
Bisulfite conversion rates were estimated using reads that uniquely aligned to the lambda phage genome and were >99% for all samples.
Analysis method
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.
Read count
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
Coverage (depth)
Oocyte-1 (amplified): 4.5x
Oocyte-2 (not amplified): 2.5x
Sperm-1: 7.6x
Sperm-2: 8.1x
Sperm-3: 8.8x
Preimplantation embryos: 23.5x
Cord blood cells-1: 3.2x
Cord blood cells-2: 3.4x
Cord blood cells-3: 3.1x
Cord blood cells-4: 3.2x
Cord blood cells-5: 3.6x
Processed data type
DNA methylation data
Data use policy
NBDC data sharing policy (JGAP000001)