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Identification of LINC00152 target genes in comparison in A172 and U87 glioblastoma cells

ABSTRACT: Identification of LINC00152 target genes in comparison in A172 and U87 glioblastoma cells

PROVIDER: PRJNA677944 | ENA |

REPOSITORIES: ENA

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Identification of LINC00152 target genes in comparison in A172 and U87 glioblastoma cells

Project description:The long noncoding RNA LINC00152 shows ubiquitous expression and is often upregulated in tumor entities compared to healthy tissues. LINC00152 promotes malignant progression in the glioblastoma cell line U87. Here, LINC00152 knockdown leads to a reduction of migration and invasion of tumor cells. However, LINC00152 seems to have an opposite effect in another glioblastoma cell line A172. For this reason, the transcriptional patterns after LINC00152 knockdown in both cell lines (U87 and A172) were compared to identify the differences.

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Transcriptome analysis of U87 cells upon LINC00152 knockdown

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Transcriptome analysis of U87 cells upon LINC00152 knockdown

Project description:To understand the global changes in genes expression after knockdown of LINC00152, we compared transcriptomes of control cells (treated with siGL2) and LINC00152 knockdown cells (treated with si00152).

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Glioblastoma Cell lines vs. Normal Glial Cells

Project description:Examination of alternative splicing in 4 glioblastoma cell lines (U118, t98g, a172, U87) vs. FGG cells grown in culture. 4 Cancer Cell lines vs. Normal Cells in a dye-swap design with 2 replicates in each dye orientation (4 tumor lines x 2 reps x 2 dye-orientations = 16 arrays)

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Transcription profiling array of human glioblastoma cell line U87 comparing control cells with U87-shLIN7a knockdown cells and rescue cells which have the same Lin7a knockdown but re-express Lin7a lentivirally (U87-shLin7a+Lin7A)

Project description:After performing an in-vivo screening with U87 glioblastoma cells transduced with a knockdown library several genes could be identified. Lin7a which was one of the candidates was further evaluated. Single knockdown of Lin7a in U87 conferred a pro-invasive phenotype in-vitro and in-vivo. Overexpression of Lin7a in the Primary glioblastoma cell line T269 reduced its invasive phenotype. To decipher the underlying pathways U87 control, U87-shLIN7a and U87-shLin7a+Lin7A (rescue cells after re-expression of Lin7A) were analyzed after in-vitro culture by a transcription profiling Array.

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Glioblastoma Cell lines vs. Normal Glial Cells

Project description:Examination of alternative splicing in 4 glioblastoma cell lines (U118, t98g, a172, U87) vs. FGG cells grown in culture. SUBMITTER_CITATION: Jonathan Gelfond, Lee Ann Zarzabal, Tarea Burton, Suzanne Burns, Mari Sogayar, Luiz O. F. Penalva. Latent rank change detection for analysis of splice-junction microarrays with nonlinear effects. Annals of Applied Statistics 2011, Vol. 5, No. 1, 364-380

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Project description:The goal of this study was to investigate the regulatory events underlying post-transcriptional changes in gene expression, and more specifically in mRNA stability, in cancer. We observed that the stability of RBFOX1 targets was decreased in glioblastoma and, given that RBFOX1 is known to stabilize its targets mRNAs, we hypothesized that RBFOX1 down-regulation is responsible at least in part for alterations in the glioblastoma transcriptome. We overexpressed RBFOX1 in the A172 human glioblastoma cell line and performed RNA-sequencing on extracted RNA. We computed differential gene expression in the cell line overexpressing RBFOX1, compared to the control samples. We confirmed that RBFOX1 overexpression leads to an upregulation of the RBFOX1 regulon, including the majority of RBFOX1 targets that are destabilized in tumors. The results suggest that RBFOX1 downregulation in glioblastoma leads to the destabilization of its targets, which can be partially rescused through overexpression of RBFOX1.

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Gene expression data in A172 cell line transfected with MED12 siRNA or its control

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