Development of gene expression signatures for glioblastoma with circ2082 knock-down (KD)
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ABSTRACT: To further develop gene expression approach, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to identify circ2082 expression effect in different subpopulations of glioblastoma cells (G cells). Cells were transfected with either control or antisense oligos targeting circ2082. KD of circ2082 affects gene expression patterns in cell subtype specific pattern
Project description:RKO Colon Carcinoma Cells were treated with 100nM of either SIM2s Control or Antisense oligos in a timecourse (10, 14, 18, 24hr) dependent manner.
Project description:Analysis of HSF1-down regulation of HCC cells at gene expression level. Results provide important information of genes involved in HSF1, such as liver proliferation, apoptosis, stress response, metabolism, these genes were up- or down-regulated. Total RNA obtained from HSF1-KD KYN2 (HCC) cells and HSF1-control KYN2 cells. To identify genes generally involved in HSF1 associated, we compared expression profiles between HSF1-KD KYN2 (HCC) cells and HSF1-control KYN2 cells by using Illumina HumanWG-6 BeadChip.
Project description:Efficient TYRP1 knock-down (KD) have been performed in human melanoma cell line expressing a high level of TYRP1 mRNA and protein in order to identify the molecular pathway explaining the decrease of cell proliferation in TYRP1 KD cells.
Project description:To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. We developed transgenic lines by antisense silencing the genes, which are expressed in the AZ to study the functional role in abscission process. In the current stuty we silenced KD gene by antisense technology under abscisson promoter (TAPG::antsisense KD). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.
Project description:To investigate the function of CDCP1 in regulation of HCF proliferation, we cultured primary HCFs and transfected with non-targeting siRNA and CDCP1 siRNAs. Total RNA samples were extracted for RNA-seq to identify transcriptome-wide gene expression changes in the HCFs after CDCP1 knock-down (KD).
Project description:293T cells are transfected with hsa_circ_0001400 expression plasmid vectors for 24 hours. Cells are then incuvated with Psoralen, exposed to long-wave UV for 10 minutes, and total RNA was extracted. Biotynilated DNA oligos sense (control) or antisense of circ_0001400 are added and circRNA-RNA complexes are enriched using streptavidin beads. RNA was cleaned and exposed to short-wave UV and subjected for RNA-Seq.
Project description:Total RNA from V703 and V481 cells (negative control vs KD of lincDUSP) were subjected to next generation RNA-seq (100bp, paired-end, strand-specific). The expression of mRNAs was calculated as FPKM values.
Project description:Colorectal cancer is one of the most common cancers. Cancer cells are highly dependent on dysregulated gene expression to support their uncontrolled growth and high energy needs. The expression of gene encoding chromodomain helicase DNA binding protein 6 (CHD6) is frequently altered in tumor tissues of colorectal cancer patients.We performed transcriptomic analysis to identify the differentially expressed genes between control and CHD6 KD HCT116.