NBDC Research ID: hum0055.v1

 

SUMMARY

Aims: To elucidate the mRNA expression related to the development and/or progression of non-alcoholic fatty liver disease (NAFLD).

Methods: RNA-seq and Methylation array analysis by using of mRNA or DNA purified from liver tissues

Participants/Materials: 64 NAFLD patients

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000059

NGS (RNA-seq)

Methylation array

Controlled Access (Type I) 2017/02/20

*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

RNA-seq

Participants/Materials Human liver tissues from NAFLD patients: 60 samples
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source mRNAs extracted from NAFLD liver tissues
Cell Lines -
Library Construction (kit name) Agilent SureSelectXT RNA Target Enrichment for Illumina Multiplexed Sequencing
Fragmentation Methods chemical fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000059
Total Data Volume 307 GB (fastq [3,516,104,874 reads / 974 files)
Comments (Policies) NBDC policy

 

Methylation array

Participants/Materials Human liver tissues from NAFLD patients: 60 samples (56 are same samples as RNA-seq)
Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina Infinium® Human Methylation 450K BeadChip
Library Source DNAs extracted from NAFLD liver tissues
Cell Lines -
Library Construction (kit name)

Bisulfite Conversion: EZ DNA Methylation™ Kit (Zymo Research)

Methylation analysis: Infinium® Human Methylation 450K BeadChip kit (Illumina)

Algorithms for Calculating Methylation-rate (software) GenomeStudio Software (Illumina)
Filtering Methods

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 of microarray 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.
Probe Number (after QC) 431,736 CpGs (on autosomal chromosomes, reference [hg19])
Japanese Genotype-phenotype Archive Data set ID JGAD00000000059
Total Data Volume 300 MB (txt)
Comments (Policies) NBDC policy

This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.

 

DATA PROVIDER

Principal Investigator: Kikuko Hotta

Affiliation: Department of Medical Innovation, Osaka University Hospital

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (C) Genetic predisposition and environmental factor retrieval of ectopic fat accumulation and their verification in prospective follow-up survey 25461343
KAKENHI Grant-in-Aid for Scientific Research (C) Elucidation of pathology and development of diagnosis method of nonalcoholic fatty liver disease by using genomic, and epigenomic analysis 16K09781
KAKENHI Grant-in-Aid for Scientific Research (C) Analysis of genetic predisposition and environmental factors related to the onset and progression of nonalcoholic fatty liver disease 26460999

 

PUBLICATIONS

TitleDOIData Set ID
1 Identification of core gene networks and hub genes associated with progression of nonalcoholic fatty liver disease by RNA sequencing doi: 10.1111/hepr.12877 JGAD00000000059
2 Identification of the genomic region under epigenetic regulation during nonalcoholic fatty liver disease progression. doi: 10.1111/hepr.12992 JGAD00000000059

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Pablo Giraudi Fondazione Italiana Fegato JGAD00000000059 2018/12/18-2018/12/31