Project description:NFX1-91, a novel E6 cellular downstream target, functions as a transcriptional regulator and is involved in repressing hTERT expression. Other functions and downstream targets regulated by NFX1-91 were not well understood. We used microarrays to determine gene expression deregulated when NFX1-91 was knocked down. HCT116 cells was infected with lentivirus carrying NFX1-91 shRNA or control β-Galactosidase shRNA to stably knock down target gene expression. Total RNAs were extracted and hybridized on Affymetrix microarrays.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to evaluate the effects of si-LINC00152 on the mRNA of human colon cancer cell line HCT116. Methods: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting LINC00152 for 36 hours in DMEM medium (with 10% serum). Total RNA were extracted and detected by Illumina high-throughput RNA sequencing data analysis. 2 independent biological replicates were plated, transfected in parallel for each control and siRNA. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 90 mRNAs were up-regulated and 159 were down-regulated in “si-LINC00152” group comparing to “control” group. Conclusions: Our study describes the mRNA changes of human colon cancer cell line HCT116 transfected with LINC00152 siRNA.
Project description:NFX1-91, a novel E6 cellular downstream target, functions as a transcriptional regulator and is involved in repressing hTERT expression. Other functions and downstream targets regulated by NFX1-91 were not well understood. We used microarrays to determine gene expression deregulated when NFX1-91 was knocked down.
Project description:Non-coding RNAs (ncRNAs) are finely tuned cellular regulators important for human cell growth and cancer progression. DUBR (also known as linc00883) is a nuclear ncRNA first discovered in mice for its role in regulating myoblast differentiation through interactions with chromatin and DNA methyltransferases. High expression levels of this ncRNA are predictive of poor patient outcome in colon adenocarcinoma, suggesting that DUBR may be involved in controlling cancer growth. To elucidate its function, we used RAP-MS and RNA immunoprecipitation techniques which revealed its interaction with epigenetic maintenance proteins in the human colon cancer cell line HCT116. Further, ATAC-seq and RNA-seq were used to address its function in regulating the epigenome and transcriptome of HCT116 cells. Here we report that DUBR is a regulator of human colon cancer cell line HCT116 survival.
Project description:P53 mutation is closely associated with the occurrence and progression of colon cancer. In this project, we did crotonylomics sequencing by using human colon cancer homologous cell line pair-HCT116+/+(with wild type p53) and HCT116-/- (with null p53). Crotonylomics sequencing results showed that p53 deficiency regulated crotonylation of non-histone proteins.
Project description:Chromatogram library generated of pooled sample. Coculture spheroids formed from fibroblast and colon cancer cell lines, and monoculture spheroids formed from the colon cancer cell line HCT116.
Project description:To identify differentially expressed genes by siRNAs transfection in human colon cancer cell line, HCT116 was subjected to Agilent whole genome microarrays.
Project description:Experimental set accompanying Giacomini et al publication "A legacy gene-expression signature of genetic instability in colon cancer". Includes 18 colon cancer cell line training set, 13 colon cancer cell line test set, and 3 cell lines (HCT116, HCT116+ch2, HCT116+ch3) used to evaluate signature after correcting underlying genetic instability. Experiments were performed by comparing mRNA from each colon cancer cell line (Cy5; channel 2) to a "universal" mRNA reference (Cy3; channel 1). A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Series type: disease_state_design Series_overall_design: Using regression correlation Keywords: other
