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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)
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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

NHA000065

Type of data
(2) Methylation rates at each CpG site from WGBS
Access criteria
Unrestricted-access
Total data volume
1.8 GB
File formats
  • XLSX
  • ZIP
Research
hum0056
Date published
2018-03-30
Date modified
2018-03-30
Secondary ID
hum0056.v1.ch3.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0056.v1.ch3.v1.zip1.8 GB
hum0056_header.xlsxDictionary file13.3 KB

Analysis method

WGBS

Materials and participants
IMM cohort: 197 individuals
  • Subject count
    197 (Individual)
Sample description
DNAs extracted from 102 monocytes, 102 CD4+ T cells, and 94 neutrophils
  • Tissue
    CD4+ T cell, Monocyte, Neutrophil
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGBS
Target
N/A
Reagent kit
TruSeq DNA Methylation Kit
Fragmentation
bisulfite conversion reaction
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
125 bp
Reference genome
GRCh37
Mapping
NovoAlign (ver.3.02.08)
Read deduplication
SAMtools (ver.0.1.19)
Realignment and base quality recalibration
none
QC and filtering
electrophoresis and qPCR
Analysis method
NovoMethyl (ver.3.02.08)
Read count
Monocytes: 780,709,034 ± 45,934,514 / 624,432,868 ± 38,766,158
CD4+ T cells: 779,212,752 ± 40,833,955 / 667,934,331 ± 33,002,407
Neutrophils: 1,144,935,054 ± 33,512,764 / 994,992,101 ± 32,667,070
Coverage (depth)
Monocytes: 31.1x (± 1.6)
CD4-positive T lymphocytes: 31x (± 1.6)
Neutrophils: 54.7x (± 1.6)
Processed data type
DNA methylation data
Data use policy
NBDC data sharing policy (JGAP000001)