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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

JGAD000059

Type of data
NGS (RNA-seq)
Methylation array
Access criteria
Controlled-access (Type I)
Total data volume
330 GB
File formats
  • FASTQ
  • TXT
Research
hum0055
Date published
2020-09-28
Date modified
2024-01-19
DDBJ Search
JGAD000059 (opens in a new tab)
JGA Study
JGAS000059 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
Human liver tissues from NAFLD patients: 60 samples
  • Health status
    Affected
  • Subject count
    60 (Sample)
Sample description
mRNAs extracted from NAFLD liver tissues
  • Tissue
    Liver
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
SureSelect XT RNA Target Enrichment
Fragmentation
chemical fragmentation
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
100 bp
Data use policy
NBDC data sharing policy (JGAP000001)

メチル化アレイ

Materials and participants
Human liver tissues from NAFLD patients: 60 samples (56 are same samples as RNA-seq)
  • Health status
    Affected
  • Subject count
    60 (Sample)
Sample description
DNAs extracted from NAFLD liver tissues
  • Tissue
    Liver
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Methylation array
Target
N/A
Reagent kit
EZ DNA Methylation Kit
Infinium HumanMethylation450 BeadChip Kit
Platform
Illumina Infinium HumanMethylation450
Reference genome
GRCh37
QC and filtering
Probes as shown below were excluded:
with intensities indistinguishable from the background (detection P-value > 0.05) in more than one sample
with a bead count < 3 in at least 5 % of samples
including any SNPs
cross-reactive
Normalization
Raw DNA methylation data were preprocessed by normalizing to appropriate internal control probes. The effects of two types of CpG probes on CpG methylation measurements were corrected using beta-mixture quantile normalization, and batch effects were corrected using a ComBat normalization method in the R/Bioconductor package ChAMP.
Analysis method
GenomeStudio Software (Illumina)
Probe count
431,736 (CpGs on autosomes)
Data use policy
NBDC data sharing policy (JGAP000001)