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RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Sox4 or a scrambled shRNA

ABSTRACT: Through RNA-sequencing we analyzed the differentially expressed genes upon in vitro knockdown of Sox4 in mouse E14.5 embryonic neural stem cells using one shRNA against Sox4

ORGANISM(S): Mus musculus

PROVIDER: GSE121173 | GEO | 2018/10/12

REPOSITORIES: GEO

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RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Foxp1 or a scrambled shRNA

Project description:Through RNA-sequencing we analysed the differentially expressed genes upon in vitro knockdown of Foxp1 in mouse E14.5 embryonic neural stem cells using one shRNA against Foxp1

2017-11-14 | GSE101605 | GEO

RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Sox4 or a scrambled shRNA

Project description:RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Sox4 or a scrambled shRNA

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RNA-sequencing of human mammary epithelial cells (HMLEs) transduced in vitro with a shRNA against SOX4 or a scrambled shRNA in untreated and TGF-β-treated (16 hours) conditions

Project description:In order to identify SOX4- and TGF-beta dependent genes, human mammary epithelial cells (HMLEs) were transduced with shRNA scrambled (control) or shRNA targeting SOX4 (TRCN0000018213, Sigma Aldrich, St. Louis, MS) and selected with puromycin for at least 2 weeks. SOX4 knockdown was confirmed by qRTPCR and western blotting. Cells were plated in 6 well plates and either left untreated or treated with TGF-beta (2.5ng/ml) for 16 hours in biological duplicate (different passages). Samples were harvested and total RNA was isolated using RNAeasy kit (Qiagen). Samples were sequenced on the NextSeq 500 (Illumina), SE75.

2018-06-11 | GSE104759 | 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

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TRPM7 maintains mesenchymal phenotype of breast cancer cells by tensional regulation of SOX4 (SOX4 shRNA)

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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

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

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

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

Identification of SOX4 novel transcriptional targets.

Project description:The SOX4 gene belongs to a family of transcription factors and we previously unveiled SOX4 gene amplification and over-expression in a subset of lung cancers, indicating it may constitute a driver oncogene. Here, we searched for SOX4 transcriptional targets and investigate their involvement in lung development and carcinogenesis. We abrogated SOX4 expression in the NIH-H522 lung cancer cell line, carrying SOX4 amplification and over-expression, using an inducible short-hairpin system. Global analysis of gene expression identified about 90 genes down-regulated after SOX4 abrogation many of them related to neural development. We also demonstrated recruitment of SOX4 to many of these promoters, evidencing their nature as direct transcriptional targets of SOX4. Most of these transcripts were significantly increased in lung cancer cells with ectopic SOX4 over-expression and in lung tumors with high levels of SOX4. Conversely, many of them exhibited significant low expression levels in embryonic fibroblasts from Sox4-/- mice. We generated H522-derived cells that down-regulate SOX4 in an inducible manner. The H522 cells were transfected with a tetracycline (tet) repressor expression construct and a tet-repressor-controlled expression vector (tet-on) containing a shSOX4. An stable clone, H522Tr-shSOX4-1, which down-regulate SOX4 expression by 90%, 48 hours after adding doxycycline, was chosen for further analysis. To determine the gene expression profile characteristic of SOX4 depleted expression we compared the global gene expression of the parental H522 cells to the H522Tr-shSOX4-1 cells at 0, 24 and 96 hrs after inducing the shSOX4 with doxycycline using the Whole Human Genome Microarray from Agilent.

2011-11-18 | E-GEOD-31612 | biostudies-arrayexpress

Expression data from LNCaP cells transfected with SOX4 cDNA, SOX4 siRNA or GFP cDNA

2008-11-10 | GSE11914 | GEO

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