|
| Status |
Public on Aug 04, 2014 |
| Title |
4 - macrophage + fibroblast & TNF |
| Sample type |
SRA |
| |
|
| Source name |
primary macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary macrophages
treatment: TNF + co-culture with fibroblast
barcode: GTGAAA
|
| Treatment protocol |
Mono- or co-cultures were then treated with or without TNFa (20ng/mL) for 2 days.
|
| Growth protocol |
Human CD14+ cells isolated from PBMCs were differentiated into macrophages for 1 day with MCSF (10ng/mL) in RPMI/10% FBS. Transwell chambers with or without synovial fibroblasts were then placed above the macrophages. (Human synovial fibroblast cell lines were generated from synovial tissue extracted during knee arthroplasty, minced and collagenase digested. Adherent cells at passage 4 or beyond were used for macrophage-fibroblast co-cultures.)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Macrophage RNA was isolated with RNAeasy mini kit (Qiagen) and polyA mRNA purified with the Truseq kit (Illumina).
Libraries were generated with the Truseq kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
M (Fib) + TNF
|
| Data processing |
The TopHat program was used to align the reads to the UCSC Hg19 human reference genome.
The Cufflinks program was used to calculate measurements of transcript abundance (represented by Fragments Per Kilobase of exon model per Million mapped reads (FPKM)).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
May 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura Donlin |
| E-mail(s) |
donlinl@hss.edu
|
| Phone |
212-774-2743
|
| Organization name |
Hospital for Special Surgery
|
| Department |
Arthritis and Tissue Degeneration Program
|
| Street address |
535 E. 70th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE57723 |
Modulation of the TNF-induced macrophage response by synovial fibroblasts |
|
| Relations |
| BioSample |
SAMN02781629 |
| SRA |
SRX544936 |
