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Series GSE57723 Query DataSets for GSE57723
Status Public on Aug 04, 2014
Title Modulation of the TNF-induced macrophage response by synovial fibroblasts
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Here we explored how the human macrophage response to tumor necrosis factor (TNF) is regulated by human synovial fibroblasts, the representative stromal cell type in the synovial lining of joints that become activated during inflammatory arthritis. Genome-wide transcriptome analysis (RNAseq) showed that co-cultured synovial fibroblasts modulate the expression of approximately one third of TNF-inducible genes in macrophages, including expression of target genes in pathways important for macrophage survival and polarization towards an alternatively activated phenotype. This work furthers our understanding of the interplay between innate immune and stromal cells during an inflammatory response, one that is particularly relevant to inflammatory arthritis. Our findings also identify modulation of macrophage phenotype as a new function for synovial fibroblasts that may prove to be a contributing factor in arthritis pathogenesis.
 
Overall design Human CD14+ MCSF-differentiated macrophages were cultured with or without synovial fibroblasts in transwell chambers. TNF was added at Day 0, macrophages were harvested at Day 2. Total of 4 samples: (1) macrophages alone (2) macrophages with fibroblasts (3) macrophages with TNF (4) macrophages with fibroblasts and TNF. Macrophage RNA was purified using RNeasy mini kit (Qiagen). Tru-seq sample preparation kits (Illumina) were used to purify poly-A transcripts and generate libraries with multiplexed barcode adaptors. All samples passed quality control on a Bioanalyzer 2100 (Agilent). Paired-end reads (50 x 2 cycles, ~75x106 reads per sample) were obtained on an Illumina HiSeq 2500. The TopHat program was used to align the reads to the UCSC Hg19 human reference genome, while the Cufflinks program allowed for measurements of transcript abundance (represented by Fragments Per Kilobase of exon model per Million mapped reads (FPKM)).
 
Contributor(s) Donlin LT, Ivashkiv LB
Citation(s) 25057003
Submission date May 16, 2014
Last update date Mar 20, 2019
Contact name Laura Donlin
E-mail 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
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1387572 1 - macrophage
GSM1387573 2 - macrophage + fibroblast
GSM1387574 3 - macrophage + TNF
Relations
BioProject PRJNA247937
SRA SRP042031

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57723_Macrophage_FPKM_allsamples.txt.gz 671.5 Kb (ftp)(http) TXT
Raw data are available in SRA
Processed data is available on Series record

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