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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
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Dataset ID

NHA000134

Type of data
Read counts for each gene detected from NGS (RNA-seq)
Access criteria
Unrestricted-access
Total data volume
21.5 MB
File formats
  • XLSX
  • ZIP
Research
hum0207
Date published
2020-01-06
Date modified
2020-01-06
Secondary ID
hum0207.v1.RNA.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0207.v1.RNA.v1.zip21.5 MB
hum0207.v1_header.xlsxDictionary file17.0 KB

Analysis method

RNA-seq

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    60 (Individual)
Disease
rheumatoid arthritis (M05)
osteoarthritis (M06)
Sample description
RNAs extracted from cells from rheumatoid arthritis and osteoarthritis patients
  • Tissue
    B cell, CD4+ T cell, CD8+ T cell, Monocyte, NK cell, Synovial fibroblast
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq Stranded mRNA Library Prep Kit
Fragmentation
Heat treatment
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
125 bp
Reference genome
GRCh37
Mapping
STAR (version 2.5.3)
Read deduplication
N/A
Realignment and base quality recalibration
N/A
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
HTSeq (version 0.6.0)
Read count
10 million - 30 million / 10 million - 30 million
Coverage (depth)
N/A
Coverage (breadth)
N/A
Gene count
58,325
Processed data type
Count data
Data use policy
NBDC data sharing policy (JGAP000001)