Data · dataset · 2025
ChIP-seq detection of transcription factor p65-enriched DNA fragments in rheumatoid arthritis patient-derived synovial fibroblasts
Listed in ScienceDB
Synovial fibroblasts were isolated from synovial tissues of rheumatoid arthritis patients, passaged, and purified, and identified by flow cytometry.
Description
Cells from passages 3 to 8 were used for experiments. Synovial fibroblasts were stimulated with TNF for 24 h.
Synovial fibroblasts (1×10⁷) were PBS-washed, cross-linked in 1% formaldehyde (10 min, room temperature), and quenched with 0.125 M glycine (5 min). After centrifugation and PBS washes, cells were lysed in ice-cold buffer (0.5% NP-40, 10 mM HEPES pH 7.5, 0.1 mM EDTA, protease inhibitors) for 5 min. Nuclei were pelleted (2000×g, 10 min, 4°C), and chromatin was sonicated to 100-500 bp fragments.
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Sonicated chromatin was divided: 10% retained as "input," 80% immunoprecipitated with anti-p65 antibody (CST #8242), and 10% incubated with rabbit IgG (Abcam ab171870) as "IgG" control. IP complexes were sequentially washed, eluted, and de-crosslinked. DNA from input and IP fractions was phenol-chloroform-extracted, quantified (Qubit 3), and quality-checked by agarose gel electrophoresis (chromatin fragmentation) and Western blot (IP efficiency).
Sequencing libraries were prepared using VAHTS Universal DNA Library Prep Kit (Vazyme ND607), size-selected (200-500 bp), and sequenced on an Illumina Novaseq X Plus (PE150 mode).
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.24038 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Medicine & Health · Social Science
- Inferred from text
- Sequencing 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.24038 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license_text | source · scidb cn | connector:scidb_cn@1.0.0 | |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |