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 ID | Type of Data | Criteria | Release 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 |
*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
| 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 |
(Click the Dataset ID to download the file) |
| Total Data Volume | 20.5 MB (txt) |
| Comments (Policies) | NBDC policy |
| 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 |
(Click the Dataset ID to download the file) |
| Total Data Volume | 158.1 MB (txt) |
| Comments (Policies) | NBDC policy |
| 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 |
(Click the Dataset ID to download the file) |
| Total Data Volume | 1.3 MB (txt) |
| Comments (Policies) | NBDC policy |
| 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 |
(Click the Dataset ID to download the 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 | DOI | Dataset 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 |
| 2 |
