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Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HA-SOX4/YFP

ABSTRACT: 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 identified the direct transcriptional targets of SOX4 using a genome-wide localization ChIP-chip analysis. Keywords: ChIP-chip

ORGANISM(S): Homo sapiens

PROVIDER: GSE11874 | GEO | 2008/11/10

SECONDARY ACCESSION(S): PRJNA109103

REPOSITORIES: GEO

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Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HA-SOX4/YFP

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 identified the direct transcriptional targets of SOX4 using a genome-wide localization ChIP-chip analysis. Keywords: ChIP-chip LNCaP prostate cancer cells were stably infected with a lentivirus containing either HA-SOX4-IRES-YFP or IRES-YFP alone. Cells were sorted for YFP expression and expanded in tissue culture before chromatin immunoprecipitation against the HA epitope tag was performed.

2008-11-09 | E-GEOD-11874 | biostudies-arrayexpress

Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HOXC6-HA/YFP

Project description:The transcription factor HOXC6 is upregulated in human prostate cancer. SiRNA knockdown of HOXC6 induces apoptosis in LNCaP cells while upregulation rescued LNCaP cells from siRNA-induced apoptosis. We used chromatin immunoprecipitaiton followed by microarray to identify the gene promoters that are bound by HOXC6 in LNCaP cells. Keywords: Stable expression and chromatin immunoprecipitation

2008-03-01 | GSE9772 | 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

Expression data from 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) Keywords: Gene Expression

2008-11-10 | GSE11914 | GEO

Illumina expression data from LNCaP cells overexpressing either SOX4 or GFP

2008-11-10 | GSE11913 | GEO

SOX4 effect on LNCaP prostate cancer cells

Project description:This SuperSeries is composed of the following subset Series: GSE11874: Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HA-SOX4/YFP GSE11913: Illumina expression data from LNCaP cells overexpressing either SOX4 or GFP GSE11914: Expression data from LNCaP cells transfected with SOX4 cDNA, SOX4 siRNA or GFP cDNA Refer to individual Series

2008-11-09 | E-GEOD-11915 | biostudies-arrayexpress

SOX4 binding profiling in mouse embryonic neural stem cells (NSCs)

Project description:By chromatin-immunoprecipitating (ChIP) SOX4 in NSCs we identified genome-wide binding sites for SOX4

2018-10-06 | GSE120894 | GEO

RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells

Project description:We identified the SOX4 transcription factor and integrin alpha V encoded by the ITGAV gene as important resistance mechanisms to T cell-mediated cytotoxicity of TNBC cells. Here, we performed RNA seq. analysis of SOX4 and ITGAV deficient (CRISPR knockout) BT549 human and 4T1 murine TNBC cells as compared to control edited counterparts. Additionally, we performed SOX4 specific ChIP-seq studies in BT549 human TNBC cells. The objective of the study was to identify the molecular regulators and signaling pathways that mediate resistance to T cell mediated immunity. GSEA analysis of RNA-seq data showed that the 'interferon response' represented one of the top pathways for genes upregulated in SOX4 or ITGAV edited compared to control TNBC cells. In contrast, gene sets associated with TGF beta and TNF alpha/NF kappa b were negatively enriched in both Sox4 and Itgav edited TNBC cells. Further analysis of RNA-seq data showed that SOX4 or ITGAV edited TNBC cells contained higher mRNA levels of many interferon-stimulated genes (ISGs), including genes associated with important innate immune pathways such as RIG-I/MDA-5, cGAS - STING and the AIM2 inflammasome

2021-01-01 | GSE144013 | GEO

SOX4 facilitates PGR protein stability and FOXO1 expression conducive for human endometrial decidualization

Project description:To detect the direct target genes of SOX4 in differentiated human endometrial stromal cells(hEnSC), differentiated hEnSC cells at the presence of MPA, E2 and cAMP are collected and subjected to ChIP-Seq. After aligned to human Hg38 by STAR, peaks are called by MACS2. Our results show that SOX4 is the key regulator for decidualization by regulating FOXO1, STAT3, PRL and FOSL2. This specific enrichment is confirmed by ChIP-qPCR. Additionally, there are also some other direct genes of SOX4, indicating the essential role of SOX4 in decidualization. This ChIP-Seq data provides fundamental information for our further physiological study of SOX4.

2022-10-05 | GSE174602 | GEO

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

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