Project description:we performed microarray expression profiling to analyze the differentially expressed genes between U251-shCtrl and U251-shCPVL cells.
Project description:ESCC tumor tissues possessed a significantly higher expression of CDKL3 than matched adjacent normal tissues. CDKL3 acts as a new oncogene in ESCC cell line TE-1. However, the molecular mechanisms and biological effects of CDKL3 in esophageal squamous cell carcinoma (ESCC) remain unknown. We used microarrays to elucidate the molecular mechanisms through which CDKL3 promotes the proliferation of ESCC cancer cells.
Project description:To explore the target genes of long noncoding RNA lncTCF7, we established lncTCF7-silenced HCC primary CSC cells and conducted transcriptome microarray analysis. We used microarrays to identify distinct gene expression underlying shCtrl and shlncTCF7 of hepatocellular carcinoma sample stem cells. We cultured shlncTCF7 and shCtrl cells from hepatocellular carcinoma (HCC) clinical sample, then hybridized on Affymetrix microarrays. We sought to identify distinct target genes of lncTCF7 in liver cancer stem cells (CSCs).
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Project description:DIDO1(Death inducer-obliterator) gene localizes in the nucleus and cytosol, which is required in the early steps during the tumor progression and metastasis. We analyzed the GeneChip expression profiles of human umbilical vein endothelial cells transfected by RNAi lentiviral vectors, shDIDO1 cell line and shCtrl cell lines
Project description:Gene expression in NCI-H1299 cells infected with shCtrl and shRPL35A was detected with a PrimeView human gene expression array. Gene expression profiling of shCtrl and shRPL35A NCI-H1299 cells was acquired and analyzed. Differentially expressed genes were identified based on fold change of mean of expression (fold change ≥ 1.3) and FDR (< 0.05) from P value calculated based on linear model of empirical Bayesian distribution. Finally, 2055 upregulated genes and 1559 downregulated genes were characterized.
Project description:To explore the target genes of long noncoding RNA lncTCF7, we established lncTCF7-silenced HCC primary CSC cells and conducted transcriptome microarray analysis. We used microarrays to identify distinct gene expression underlying shCtrl and shlncTCF7 of hepatocellular carcinoma sample stem cells.