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SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes

ABSTRACT: SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes

PROVIDER: PRJNA811584 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18148863.fastq.gz	Fastqsanger.gz
	SRR18148864.fastq.gz	Fastqsanger.gz
	SRR18148865.fastq.gz	Fastqsanger.gz
	SRR18148866.fastq.gz	Fastqsanger.gz
	SRR18148867.fastq.gz	Fastqsanger.gz

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SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [ChIP-Seq]

Project description:Purpose: 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.

2022-03-21 | GSE197491 | GEO

SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [RNA-Seq]

Project description:SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [RNA-Seq]

| PRJNA811590 | ENA

SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [ChIP-Seq]

Project description:SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [ChIP-Seq]

| PRJNA810559 | ENA

SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [RNA-Seq]

Project description:Purpose: Our goal was to evaluate the transcriptional profiles of FLS. We used genome wide approaches to uncover the interactions between SOXC transcription factors and RELA/p65 transcription factor, downstream of TNF signaling. Methods: We analyzed RNA-seq of TNF-treated FLS in control and SOXC gene knockout backgrounds. FLS isolated from Sox4fl/fl 11fl/fl 12fl/fl mice were transduced with Ade5CMV-eGFP virus for controls or transduced with Ade5CMV-Cre adenovirus for knockout of the three SOXC family genes, Sox4, Sox11 and Sox12 Results: paired-end reads were mapped to the mm10 genome assembly. RNA levels were normalized using DESeq. Conclusion: SOXC family genes regulate TNF mediated gene expression.

2022-03-21 | GSE197691 | GEO

SOX4 and RELA Function as Transcriptional Partners to Regulate the Expression of TNF- Responsive Genes in Fibroblast-Like Synoviocytes.

Project description: Not available

| S-EPMC9074688 | biostudies-literature

SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-03-21 | GSE197694 | GEO

TNF treated Synoviocytes

Project description:Time series of human arthritic synoviocytes treated with TNFalpha. Keywords: time-course

2003-07-03 | GSE516 | GEO

Transcription profiling of human arthritic TNF treated synoviocytes

Project description:Time series of human arthritic synoviocytes treated with TNFalpha.

2008-06-13 | E-GEOD-516 | biostudies-arrayexpress

Expression data for T24 bladder cancer cell line - scrambled, SOX4-KD and SOX4 overexpression

Project description:We knocked down SOX4 in T24 cell and created 3 cell lines: T24-scrambled, T24-SOX4-knockdown and T24-SOX4-rescue and compared gene expression changes SOX4 is a developmental transcription factor that is overexpressed in as many as 23% of bladder cancer patients, but the role of SOX4 in bladder cancer tumorigenesis is not well understood. Given SOX4’s many roles in embryonic development and context-dependent regulation of gene expression, we sought to understand SOX4’s contribution to bladder cancer and to elucidate SOX4 regulated genes that might contribute to tumorigenesis. We employed a CRISPR interference (CRISPRi) method to transcriptionally repress SOX4 expression in T24 bladder cancer cell lines, rescued these cell lines with lentivirally expressed SOX4, and performed whole genome expression profiling. SOX4 knockdown cells exhibited decreased invasive capabilities but no changes in migration or proliferation, while rescue with SOX4 lentiviral vector restored the invasive phenotype. Gene expression profiling revealed 173 high confidence SOX4 regulated genes

2018-08-16 | GSE118572 | GEO

siRNA profiling of human LNCaP cells transfected with SOX4 cDNA, SOX4 siRNA or GFP cDNA

Project description:SOX4 is a critical developmental transcription factor in vertebrates and is required for precise differentiation and proliferation in multiple tissues. In addition, SOX4 is overexpressed in many human malignancies, but the precise role of SOX4 in cancer progression is not well understood. Here we have either eliminated SOX4 using siRNA or overexpressed a SOX4 cDNA and compared the gene expression patterns against control GFP transfections to identify SOX4 target genes. Data described in manuscript P. Liu et al., Cancer Res 46, 4011 (April 15, 2006) Experiment Overall Design: LNCaP prostate cancer cells were transfected with either a SOX4 cDNA, a pool of SOX4 siRNAs or a control GFP expression vector. Each transfection was performed in duplicate on two separate days. Total RNA was harvested 24 hours post-transfection

2008-11-14 | E-GEOD-11914 | biostudies-arrayexpress

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