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
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000059 | Controlled-access (Type I) | 2017/02/20 |
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MOLECULAR DATA
| 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 Dataset ID | JGAD000059 |
| Total Data Volume | 307 GB (fastq [3,516,104,874 reads / 974 files) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID | JGAD000059 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 | JGAD000059 |
| 2 | Identification of the genomic region under epigenetic regulation during nonalcoholic fatty liver disease progression. | doi: 10.1111/hepr.12992 | JGAD000059 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Pablo Giraudi | Fondazione Italiana Fegato | JGAD000059 | 2018/12/18-2018/12/31 | ||
| Masanori Nojima | The Institute of Medical Science, The University of Tokyo | JGAD000059 | 2019/01/21-2022/03/31 | ||
| Robert Tsai | Institute of Biosciences & Technology, Texas A&M Health Science Center | Genome-wide Discovery of new Plasma DNA Mehylation Makers for Tracking the Progression of NAFLD to NASH and HCC | JGAD000059 | 2020/11/06-2022/08/31 | |
| Kikuko Hotta | Laboratory of Pathophysiology and Pharmacotherapeutics Faculty of Pharmacy, Osaka Ohtani University | Genomic and epigenomic analysis of liver disease (nonalcoholic fatty liver disease, virus hepatitis, alcoholic hepatitis, cirrhosis, and hepatocellular carcinoma) | JGAD000059 | 2021/11/05-2024/03/31 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000059 | 2022/12/26-2025/03/31 |
