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Dataset ID

NHA000132

Type of data
Peaks from NGS (ChIP-seq)
Access criteria
Unrestricted-access
Total data volume
166 MB
File formats
  • XLSX
  • ZIP
Research
hum0207
Date published
2020-01-06
Date modified
2020-01-06
Secondary ID
hum0207.v1.ChIP.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0207.v1.ChIP.v1.zip166 MB
hum0207.v1_header.xlsxDictionary file17.0 KB

Analysis method

ChIP-seq

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    40 (Individual)
Disease
rheumatoid arthritis (M05)
osteoarthritis (M06)
Sample description
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.
  • Tissue
    B cell, CD4+ T cell, CD8+ T cell, Monocyte, NK cell, Synovial fibroblast
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
ChIP-seq
Target
N/A
Reagent kit
ChIP-IT High Sensitivity Kit
ChIP-IT PBMC Kit
Fragmentation
Ultrasonic fragmentation (Covaris S2)
Platform
Illumina HiSeq 2500
Read type
Single-end
Read length
50 bp
Reference genome
GRCh37
Mapping
Bowtie2
QC and filtering
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)
Analysis method
MACS 2.0
Read count
20-50 million
-
Coverage (depth)
N/A
Coverage (breadth)
N/A
Processed data type
Peak calls
Data use policy
NBDC data sharing policy (JGAP000001)