NBDC Research ID: hum0207.v1

 

SUMMARY

Aims: To elucidate the dynamics of synovial fibroblasts and its association with rheumatoid arthritis pathogenesis.

Methods: Synovial fibroblasts from rheumatoid arthritis and osteoarthritis patients (as a control) were stimulated with 9 cytokine conditions (IFN-α, IFN-γ, TNF-α, IL-1β, IL-6/sIL-6R, IL-17, TGF-β1, IL-18 and the mixture of these 8 cytokines [8-mix] which simulate synergistic inflammatory environment in arthritic joints) for 24 hours. Five subsets of peripheral blood mononuclear cells (CD4+ T, CD8+ T, B, NK and monocytes) were collected from the same patients. The integrative analysis including expression quantitative trait loci (eQTL) was performed with genome, transcriptome and epigenome data.

Participants/Materials: Patients with rheumatoid arthritis or osteoarthritis

 

Dataset IDType of DataCriteriaRelease Date
hum0207.v1.RNA.v1 Read counts for each gene detected from NGS (RNA-seq) Unrestricted-access 2020/01/06
hum0207.v1.ChIP.v1 Peaks from NGS (ChIP-seq) Unrestricted-access 2020/01/06
hum0207.v1.HiC.v1 Loops from NGS (Hi-C) Unrestricted-access 2020/01/06
hum0207.v1.eQTL.v1 eQTL Unrestricted-access 2020/01/06

*Release Note

*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more

 

MOLECULAR DATA

hum0207.v1.RNA.v1

Participants/Materials:

rheumatoid arthritis (ICD10: M05): 30 cases

osteoarthritis (ICD10: M06): 30 cases

5 fractions of PBMCs (CD4+ T, CD8+ T, B, NK and monocytes) and 10 conditions of synovial fibroblasts (unstimulated, IFN-α, IFN-γ, TNF-α, IL-1β, IL-6/sIL-6R, IL-17, TGF-β1, IL-18 and 8-mix) for 1 case each: total 856 samples (44 samples were excluded because of QC)

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from cells from rheumatoid arthritis and osteoarthritis patients
Cell Lines -
Library Construction (kit name) TruSeq Stranded mRNA Library Prep Kit
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 125 bp
QC adapter trimming: cutadapt, quality trimming: fastxtoolkit (bases with quality score < 20 were excluded, reads with base number < 50 were excluded, reads including 20% or more of bases with quality score < 20 were excluded)
Deduplication -
Calibration of re-alignment and base quality -
Mapping Methods STAR (version 2.5.3)
Reference Genome Sequence GENCODE v27 (GRCh37 version)
Coverage (Depth) -
Detecting Methods for Transcripts HTSeq (version 0.6.0)
Total Reads / Uniquely Mapped Reads 10 million - 30 million / 10 million - 30 million
Gene Numbers 58,325
NBDC Dataset ID

hum0207.v1.RNA.v1

(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 20.5 MB (txt)
Comments (Policies) NBDC policy

 

hum0207.v1.ChIP.v1

Participants/Materials:

rheumatoid arthritis (ICD10: M05): 20 cases

osteoarthritis (ICD10: M06): 20 cases

5 fractions of PBMCs (CD4+ T, CD8+ T, B, NK and monocytes) and 10 conditions of synovial fibroblasts (unstimulated, IFN-α, IFN-γ, TNF-α, IL-1β, IL-6/sIL-6R, IL-17, TGF-β1, IL-18 and 8-mix) were prepared for 1 case each. Samples under the same condition were pooled and immunoprecipitated with 3 anti-histone antibodies (H3K4me1, H3K4me3, H3K27ac): total 83 samples (7 samples were excluded because of QC)

Targets ChIP-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source DNAs were extracted from cells from rheumatoid arthritis and osteoarthritis patients. Then, samples under the same condition were pooled and immunoprecipitated with anti-histone antibodies.
Cell Lines -
Library Construction (kit name) CHIP-IT High Sensitivity Kit (Active Motif), CHIP-IT PBMC Kit (Active Motif)
Fragmentation Methods Ultrasonic fragmentation (Covaris S2)
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 50 bp
QC adapter trimming: cutadapt, quality trimming: fastxtoolkit (bases with quality score < 20 were excluded, reads with base number < 50 were excluded, reads including 20% or more of bases with quality score < 20 were excluded)
Mapping Methods Bowtie2
Reference Genome Sequence hg19/GRCh37
Coverage (Depth) -
Detecting Methods for peaks MACS 2.0
Total Reads / Uniquely Mapped Reads
Gene Numbers 20 million - 50 million / -
NBDC Dataset ID

hum0207.v1.ChIP.v1

(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 158.1 MB (txt)
Comments (Policies) NBDC policy

 

hum0207.v1.HiC.v1

Participants/Materials:

rheumatoid arthritis (ICD10: M05): 7 case

3 conditions of synovial fibroblasts (unstimulated, TNF-α, and 8-mix) were prepared for 1 case each. Samples under the same condition were pooled : total 3 samples

Targets Hi-C
Target Loci for Capture Methods -
Platform Illumina [HiSeq series]
Library Source DNAs extracted from pooled cells from rheumatoid arthritis patient
Cell Lines -
Library Construction (kit name) Nextera Mate Pair Sample Preparation Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris S2)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
QC performed at "juicer" software
Mapping Methods BWA-mem
Reference Genome Sequence hg19/GRCh37
Coverage (Depth) -
Detecting Methods for loops HiCCUPS
Total Reads / Uniquely Mapped Reads 370 million - 400 million
NBDC Dataset ID

hum0207.v1.HiC.v1

(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 1.3 MB (txt)
Comments (Policies) NBDC policy

 

hum0207.v1.eQTL.v1

Participants/Materials

rheumatoid arthritis (ICD10: M05): 30 cases

osteoarthritis (ICD10: M06): 30 cases

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Illumina [Infinium OmniExpressExome BeadChips]
Source DNAs extracted from cells from rheumatoid arthritis and osteoarthritis patients
Cell Lines -
Genotype Call Methods (softwares) IMPUTE2
Filtering Methods SNP call rate > 0.99, HWE < 1 × 10-6, sample call rate > 0.98
Marker Numbers (after QC) 595,693 SNVs
Reference Genome Sequence 1000 Genomes Phase 3 panel
eQTL detection method QTLtools, Meta-Tissue software
NBDC Dataset ID

hum0207.v1.eQTL.v1

(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 53.1 MB (txt)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Keishi Fujio

Affiliation: Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo

Project / Group Name: Association study between gene polymorphism and gene expression in human immune cells

Funds / Grants (Research Project Number):

Name Title Project Number
KAKENHI Grant-in-Aid for Scientific Research (B) Analysis of epigenetic structure responsible for inflammatory mediator production from rheumatoid arthritis synovial fibroblast 18H02846
KAKENHI Grant-in-Aid for Scientific Research (C) Analysis of signaling pathways identified by transcriptome analysis of rheumatoid arthritis samples 17K09972
Joint research fund (Takeda Pharmaceutical Company Limited) Construction of integrated disease database and its clinical application -
Joint research fund (Takeda Pharmaceutical Company Limited) Search for drug targets and development of therapeutic methods based on eQTL -

 

PUBLICATIONS

Title DOIDataset ID
1 Parsing multiomics landscape of activated synovial fibroblasts highlights drug targets linked to genetic risk of rheumatoid arthritis doi: 10.1136/annrheumdis-2020-218189

hum0207.v1.RNA.v1

hum0207.v1.ChIP.v1

hum0207.v1.HiC.v1

hum0207.v1.eQTL.v1

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