Next Generation Sequencing of MCF-7 and MDA-MB-435 cells
ABSTRACT: Human breast cancer cells MDA-MB-435 had higher metastatic potential and other aggressive characteristics than MCF-7 cells. Next-generation RNA sequencing (RNA-Seq) was used to clear this concern through comparison the transcriptomic expression profiles of these two cells. Total RNA were extracted from MCF-7 and MDA-MB-435S cells, and the polyA+ mRNA was sequenced using Illumina Genome Analyzer IIx. The reads were mapped to RefSeq RNA reference sequences.
Project description:This experiment performed RNA-seq of transcriptome and translatome (translating mRNA) of Caco-2 cells We extracted transcriptome and translatome from Caco-2 cells and deep sequenced them
Project description:RNA sequencing technology has been carried out in order to evaluate mRNA expression changes after manipulation of miR-23b in both MCF-7 and MDA-MB-231 breast cancer cell lines Our study implicates miR-23b in cytoskeletal remodeling in breast cancer. To evaluate the entire set of genes modulated by miR-23b we performed RNA-seq after ectopic manipulation of this miRNA in breast cancer cell lines. We over-expressed this miRNA in MCF-7 epithelial cancer cell lines and also reduced its activity by stably transfecting MDA-MB-231 mesenchymal-like cancer cell lines with a specific sponge vector. RNA-seq analysis revealed a number of candidate targets of this miRNA.
Project description:In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By employing three types of RNA-seq methods, we experimentally and computationally resolved elongation speed at individual gene level and under physiological condition in human cells. We proposed the elongation velocity index (EVI) as a relative measure and successfully distinguished slow-translating genes from the background translatome. The proteins encoded by the low-EVI genes are more stable than the proteome background. In normal cell and lung cancer cell comparisons, we found that the relatively slow-translating genes are relevant to the maintenance of malignant phenotypes. In addition, we identified cell-specific slow-translating codons, which may serve as a causal factor of elongation deceleration. We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.
Project description:Transcriptional profiling of breast cancer cells comparing pre-control transfected cells with cells transfected with pre-miR-125b. We searched for miR-125b targets by systematic screening of mRNA profiling of pre-miR-125b transfected MCF-7 cells and MDA-MB-435 cells. Overall design: Two-condition experiment, pre-miR-125b Transfected vs. pre-control Transfected MCF-7 cells. One replicate per array.
Project description:Transcriptional profiling of breast cancer cells comparing pre-control transfected cells with cells transfected with pre-miR-125b. We searched for miR-125b targets by systematic screening of mRNA profiling of pre-miR-125b transfected MCF-7 cells and MDA-MB-435 cells. Two-condition experiment, pre-miR-125b Transfected vs. pre-control Transfected MCF-7 cells. One replicate per array.
Project description:The long-term goal of our study is to understand the genetic and epigenetic mechanisms of breast cancer metastasis in human and to discover new possible genetic markers for use in clinical practice. We have used microarray technology (Human OneArray microarray, phylanxbiotech.com) to compare gene expression profiles of non-invasive MCF-7 and invasive MDA-MB-231 cells exposed to dioscin (DS), a steroidal saponin isolated from the roots of wild yam, (Dioscorea villosa). Initially the differential expression of genes (DEG) was identified that followed pathway enrichment analysis (PEA). Of the genes queried on OneArray, we identified 4641 DEG changed between MCF-7 and MDA-MB-231 cells (vehicle-treated) with cut-off log2 |fold change|≧ 1. Among these genes, 2439 genes are upregulated and 2002 genes are downregulated. DS exposure (2.30 M, 72 h) to these cells identified 801 (MCF-7) and 96 (MDA-MB-231) DEG that showed significant difference compared to untreated cells (p<0.05). Within these gene sets, DS is able to upregulate 395 genes and downregulate 406 genes in MCF-7 and upregulate 36 and downregulate 60 genes in MDA-MB-231 cells. Further comparison of DEG between MCF-7 and MDA-MB-231 cells exposed to DS identified 3626 DEG of which 1700 were upregulated and 1926 genes were down-regulated. From PEA, 12 canonical pathways were significantly altered between these two cell lines (MCF-7 and MDA-MB-231). However, no alteration in any of these pathways was noticed in MCF-7 cell, while in MDA-MB-231 cells only MAPK pathway showed significant alteration. When PEA comparison was made on DS exposed cells, it was observed that only 2 pathways were significantly affected. Further, to identify shared DEG, which are targeted by DS and overlapped in both MCF-7 and MDA-MB-231 cells, we performed intersection analysis (Venn diagram). We found that only 7 DEG are overlapped of which six are reported in the database. This study highlights the diverse gene networks and pathways through which DS exhibits its effect on breast cancer cells. Two condition experiment. Human breast cancer Cell line MCF-7 groups: Vehicle control and dioscin treated; Human breast cancer cell line MDA-MB-231 cell group; vehicle control and dioscin-treated. Biological replicates: MCF-7 control compared to MCF-7 dioscin treated; MDA-MB-231 control compated to MDA-MB-231 dioscin-treated; MCF-7 control compared to MDA-MB-231 control; MCF-7 dioscin treated compared to MDA-MB-231 dioscin-treated. duplicate array
Project description:This study aimed to further our understanding of the role that CXCR6 plays in breast cancer progression. Microarrays were searched for some genes that had correlated expression with CXCR6 mRNA. According to fold-change screening between restoring expression of CXCR6 and its respective control cells in MDA-MB-231 and MCF-7 cells, both up-regulated and down-regulated genes were shown. The restoring of CXCR6 expression in MDA-MB-231 and MCF-7 cells were respectively noted as MDA-MB-231-CXCR6 and MCF-7-CXCR6 cells and the respective controls were noted as MDA-MB-231-GFP and MCF-7-GFP cells.
Project description:RNA-Seq profiling of MCF-7 and MDA-MB-231. We profiled RNA expression in the estrogen-receptor-positive (ER+) MCF-7 and the triple-negative MDA-MB-231 breast cancer cells. The objective was to find genes differentially expressed between these cell lines as potential drivers of invasiveness of the triple-negative MDA-MB-231. We further utilized the identified differential genes to validate expression-responsive module of non-canonical Wnt signaling pathway. Overall design: 2 biological replicates of MCF-7 and 3 biological replicates of MDA-MB-231
Project description:We investigated the differentially expressed genes between MCF-7 and MCF-7-14, and estimated the similarities of expression profiles between MCF-7-14 and MDA-MB-231. We identified genes differentially expressed between non-invasive/non-metastatic and invasive/metastatic breast cancer cells. Experiment Overall Design: We performed microarray analysis as following design: MCF-7 versus MCF-7-14 versus MDA-MB-231 cells.
Project description:We investigated the differentially expressed genes between MCF-7 and MCF-7-14, and estimated the similarities of expression profiles between MCF-7-14 and MDA-MB-231. We identified genes differentially expressed between non-invasive/non-metastatic and invasive/metastatic breast cancer cells. Overall design: We performed microarray analysis as following design: MCF-7 versus MCF-7-14 versus MDA-MB-231 cells.