ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/071/SRR18148871/SRR18148871.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/072/SRR18148872/SRR18148872.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/070/SRR18148870/SRR18148870.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/069/SRR18148869/SRR18148869.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/067/SRR18148867/SRR18148867.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/068/SRR18148868/SRR18148868.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/066/SRR18148866/SRR18148866.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/065/SRR18148865/SRR18148865.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/063/SRR18148863/SRR18148863.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR181/064/SRR18148864/SRR18148864.fastq.gzprimaryOK200GenomicsBhattaram Lab, Orthopaedics, Emory Universityhttps://www.ebi.ac.uk/ena/browser/view/PRJNA810559Mus musculusxref:PubMed:35529852Purpose: Our goal was to evaluate the transcriptional profiles of FLS. We used genome wide approaches to uncover the interactions between SOX4 and RELA/p65, downstream of TNF signaling. Methods: ChIP-seq of mouse FLS was used to compare the global DNA binding profiles of SOX4 and RELA. Results: ChIP-seq revealed an overllap of SOX4 peak summits with RELA peak summits suggesting that both proteins bind in close-proximity on regulatory sequences, enabling them to co-operatively regulate gene expression. By integrating the ChIP-seq results with RNA-seq from SoxC-knockout FLS we identified a set of TNF-responsive genes that are targets of the RELA-SOX4 transcriptional complex. Conclusion: SOX4 and RELA, together orchestrate a multimodal regulation of gene expression downstream of TNF signaling. Their interdependent activities play a pivotal role in the transformation FLS in arthritis and in the inflammatory pathology of diverse tissues where RELA and SOX4 are co-expressed. Overall design: ChIP-seq of mouse FLS was used to compare the global DNA binding profiles of SOX4 and RELA.ENAfalseSOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [ChIP-Seq]SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [ChIP-Seq]2025-09-242022-03-22PRJNA810559GSE1974911009035529852