|
| Status |
Public on Apr 29, 2019 |
| Title |
ATAC_FLS_T72_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Rheumatoid Arthritis (RA) patient derived Fibroblast-like Synoviocytes
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: TNF (72hr)
tissue: RA Synovial Fluid
cell type: Fibroblast
|
| Treatment protocol |
Cells were treated with or without TNF (20ng/ml) and I-BET(10ng/ml) at various time points (1h, 3h, 6h, 24h, 48h, 72h).
|
| Growth protocol |
Fiborbloast-like synoviocytes were obtained from RA patients who underwent total knee replacement or elbow synovectomy (protocol approved by the Institutional Review Board of the Hospital for Special Surgery). Synovial tissue fragments were incubated with Liberase and fibroblast-like synoviocytes (FLS) cells were allowed to adhere to tissue culture dishes and passaged every 3-5 days (4-5 passages).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ATAC-seq
|
| Data processing |
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 or CASAVA with default parameters.
Genome_build: hg19
|
| |
|
| Submission date |
Mar 20, 2019 |
| Last update date |
Apr 30, 2019 |
| Contact name |
Christopher Loh |
| E-mail(s) |
[email protected]
|
| Phone |
6076973165
|
| Organization name |
Hospital for Special Surgery
|
| Department |
Research
|
| Lab |
Ivashkiv
|
| Street address |
515 E 71st ST
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE128644 |
TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis [ATAC-seq] |
| GSE128645 |
TNF-induced Inflammatory Genes Escape Repression in Fibroblast-like Synoviocytes: Transcriptomic and Epigenomic Analysis |
|
| Relations |
| BioSample |
SAMN11179538 |
| SRA |
SRX5549092 |
