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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.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

NHA000133

Type of data
Loops from NGS (Hi-C)
Access criteria
Unrestricted-access
Total data volume
1.4 MB
File formats
  • XLSX
  • ZIP
Research
hum0207
Date published
2020-01-06
Date modified
2020-01-06
Secondary ID
hum0207.v1.HiC.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0207.v1.HiC.v1.zip1.4 MB
hum0207.v1_header.xlsxDictionary file17.0 KB

Analysis method

Hi-C

Materials and participants
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
  • Health status
    Affected
  • Subject count
    7 (Individual)
Disease
rheumatoid arthritis (M05)
Sample description
DNAs extracted from pooled cells from rheumatoid arthritis patient
  • Tissue
    Synovial fibroblast
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Hi-C
Target
N/A
Reagent kit
Nextera Mate Pair Sample Preparation Kit
Fragmentation
Ultrasonic fragmentation (Covaris S2)
Platform
Illumina HiSeq
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
BWA-mem
QC and filtering
performed at "juicer" software
Analysis method
HiCCUPS
Read count
370 million - 400 million
Coverage (depth)
N/A
Coverage (breadth)
N/A
Processed data type
Hi-C loops
Data use policy
NBDC data sharing policy (JGAP000001)