Project description:MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5’-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. MDA-MB-231 cells were transduced with shRNAs against ELOVL5 and luciferase genes. Small RNA sequencing was used to study the cleavage profiles of shRNAs.
Project description:Identification of changes in protein expression by label-free shotgun proteomics in breast cancer MDA-MB-231 cells with knockdown of ELOVL5 and IGFBP6 genes in comparison with control MDA-MB-231 cells.
Project description:Dicer, RNase III endonuclease, is an essential enzyme in miRNA biogenesis that regulates target gene expression, and it has been reported that aberrant expressions of Dicer associate with the clinical outcomes of patients in various cancers. To explore the miRNA differencial expression regulated by Dicer in MDA-MB-231/E1A cells, the microarray profiling analysis was employed to conduct differentially expressed miRNAs in stable MDA-MB-231/vector, MDA-MB-231/E1A, and MDA-MB-231/E1A/shDicer cells.
Project description:RNA-Sequencing of basal subtype triple negative breast cancer cells, MDA-MB-231. MDA-MB-231 cells were lentivirally transduced with pLKO short-hairpin (sh) luciferase control or shZnf148 in triplicates. Differentially expressed genes by the shRNA compared to the control were determined.
Project description:To identify MBNL1-dependent changes in gene expression, MDA-MB-231 cells expressing either control or MBNL1-targeting shRNAs were transcriptomically profiled.
Project description:Dicer, RNase III endonuclease, is an essential enzyme in miRNA biogenesis that regulates target gene expression, and it has been reported that aberrant expressions of Dicer associate with the clinical outcomes of patients in various cancers. To explore the miRNA differencial expression regulated by Dicer in MDA-MB-231/E1A cells, the microarray profiling analysis was employed to conduct differentially expressed miRNAs in stable MDA-MB-231/vector, MDA-MB-231/E1A, and MDA-MB-231/E1A/shDicer cells. The four groups including vector control, E1A-expressing and Dicer knockdown in E1A-expressing MDA-MB-231 cells were harvested and RNA were isolated. Two independent experiments were performed for each group.
Project description:Identification of genes that are involved in self-seeding by comparing gene expression profiles between parental MDA-MB-231 cells and seeder cells (MDA-231-S1a and S1b) 2 replicates from each sample (parental MDA-MB-231, MDA-MB-231 S1a and MDA-MB-231 S1b) were analyzed
Project description:Abstract: RNA editing has emerged as novel mechanisms involved in cancer progression. Despite the phenotypic implications of ADAR in several cancer models, the role of ADAR on DNA damage response (DDR) and proliferation in breast cancer (BC) has not been fully addressed. To evaluate the effect of ADAR expression, MDA-MB-231 cells were transduced (MOI:200) with commercial pre-package adenoviral particles coding for ADARp110 or transduced (MOI:200) with eGFP control adenovirus. 16 h after transduction media was changed and RNA were extracted 48 h after transduction. ADARp110 overexpression produces a significant increase in transcripts related with cell cycle and proliferative pathways, in addition to other pathways related to IL10 signaling, among others. In other hand 657 sites significantly increase their editing in MDA-MB-231 OV cells at site level comparison. Conversely, transcripts involved in Generic Transcription, cell cycle, HIV life Cycle related pathways and Apoptosis suffer an increased editing ratio, suggesting that ADAR activity could be is in the regulation of the targets that bears significant changes in their editing pattern after ADAR manipulation
Project description:Identification of genes that are involved in self-seeding by comparing gene expression profiles between parental MDA-MB-231 cells and seeder cells (MDA-231-S1a and S1b)
Project description:MDA-MB-231 stable cell lines transfected with control shRNA or TIP-1 shRNA were cultured overnight. Total RNA of these cell lines was isolated for microarray analysis. Try to get more information about the difference in the mRNA levels in these cell lines. We analyzed gene expression from 6 samples: 2 control MDA-MB-231 (two independent clones) and 4 shRNA TIP-1 MDA-MB-231 cells (2 different shRNAs to silence TIP-1 expression, each shRNA has two independent clones). We used the Affymetrix Human Gene 1.0 ST platform. Array data was processed by the Affymetrix Exon Array Computational Tool. No technical replicates were performed.