SOX4 genome binding targets in glioblastoma cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE51663 | GEO | 2014/10/20
SECONDARY ACCESSION(S): PRJNA224286
REPOSITORIES: GEO
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Project description:Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle Examination of SOX4 binding profile in prostate cell LN229-SOX4 with LN229-GFP as negative control.
2014-10-20 | E-GEOD-51663 | biostudies-arrayexpress
Project description:Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle We used microarrays to detail the global programme of gene expression in SOX4 overexpression LN229 cells compared with mock control LN229 cells SOX4 overexpression LN229 cells and and control LN229 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes regulated by SOX4 in glioblastoma cell lines.
2014-09-30 | E-GEOD-51301 | biostudies-arrayexpress
Project description:Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle We used microarrays to detail the global programme of gene expression in SOX4 overexpression LN229 cells compared with mock control LN229 cells
2014-09-30 | GSE51301 | GEO
Project description:Overexpression of miR-127-3p in LN229 glioblastoma cells promotes their migration and invasion in vitro and in vivo in xenograft models. We used microarrays to detail the global programme of gene expression in miR-127-3p overexpression LN229 cells compared with mock overexpression LN229 cells MiR-127-3p overexpression LN229 cells and and mock overexpression LN229 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes regulated by miR-127-3p in glioblastoma cell lines.
2014-09-01 | E-GEOD-50173 | biostudies-arrayexpress
Project description:Overexpression of miR-127-3p in LN229 glioblastoma cells promotes their migration and invasion in vitro and in vivo in xenograft models. We used microarrays to detail the global programme of gene expression in miR-127-3p overexpression LN229 cells compared with mock overexpression LN229 cells
2014-09-01 | GSE50173 | GEO
Project description:DNA hydroxymethylation is frequently lost in glioblastoma. We hypothesized that reduced 5hmC levels might be related to the impaired expression of TET proteins in brain tumors. In this study we performed a genome-wide methylation analysis of LN229 cells stably transfected with scramble or TET3 overexpressing vectors. TET3 overexpression partially restored the genome-wide patterns of 5hmC characteristic of control brain samples in glioblastoma cell lines.
2018-03-03 | E-MTAB-6001 | biostudies-arrayexpress
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
Project description:In order to identify genes co-bound by SOX4 and SMAD3 in the context of breast cancer, different breast cell lines (HMLEs, MDA-MB-231 or HCC-1954) were used. Due to low endogenous expression levels for SOX4 in HMLEs in untreated conditions, doxycycline-dependent SOX4 overexpression was obtained by transducing HMLE cells with pIINDUCER21-SOX4 vector..Cells were plated and SOX4 and SMAD3 chromatine-immunoprecipitation was performed in untreated conditions, TGF-beta (2.5ng/ml), doxycycline (0.5ug/ml) or both as indicated. Genome-wide binding sites for SOX4 and SMAD3 was identified in HMLEs, MAD-MB-231 and HCC-1954 cells.
2018-06-11 | GSE104760 | GEO
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.
2011-11-18 | GSE31612 | GEO
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