Project description:mRNA was sequenced from HCT116 MYC 3' TBE1 (WT) and KO cells to identify genes differentially expressed after deletion of the MYC 3' TBE1
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment. Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, 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 RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection,Tumor tissue were isolated from infected recipients,and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer,especially for cell adhension
Project description:Purpose: The goals of this study are to compare the transcriptome profiling (RNA-seq) of different A20 expression in HCT116 cells, to find potiential target genes for A20 mediated immnue escape. Results: There were 352 genes altered after A20 was knocked out with the log-fold >2 or <-2 compared to WT cells, and p value<0.01 . And 143 genes changed after rescued the expression of A20 in A20-KO cells compared to A20-KO cells. Among these altered genes, 13 genes were changes consistently. Conclusion:Gain- and loss-A20 functional studies proved that A20 could decrease the ¡°eat-me¡± signal calreticulin (CRT) protein on cell membranes via stabilizing stanniocalcin 1 (STC1). Mechanistically, A20 inhibited the degradation of STC1 protein which could capture the CRT inside cell rather than to translocated to cell membrane.
Project description:Gene expression profiles were obtained via Nanostring nCounter Expression Assay (PanCancer Progression Panel, Nanostring Technologies, Hamburg, Germany). We aimed to obtain a gene expression signature associated to the kockout of p21 (i.e. Cyclin Dependent Kinase Inhibitor 1A, CDKN1A) in colorectal carcinoma samples and its association with of epithelial-mesenchymal transition (EMT). We analysed and compared three independent cultures of HCT116 p21 wt cells and three HCT116 p21-/- ko cells.
Project description:Gene expression profiles were obtained via NanoString nCounter Gene Expression Assay (PanCancer Progression Panel, XT_PGX_HuV1_CancerProg_CSO, cat. no. XT-CSO-PROG1-12, NanoString Technologies, Hamburg, Germany). We aimed to decipher the role of activating transcription factor 2 (ATF2) in colorectal cancer, so-far masked by high intratumoral heterogeneity (ITH). To overcome ITH, we generated monoclonal ATF2 knockout (KO) cells (termed F9 and E5) using CRISPR/Cas9 gene editing and analyzed alterations of their gene expression profiles in comparison to the parental HCT116 cell line (HCT116 WT).