Human Breast Cells: Control vs. TRIM29 cDNA- or TRIM29 shRNA-transfected
ABSTRACT: Transcriptional profiling of human normal-like breast cells MCF10A comparing control MCF10A cells transfected with a pLenti6/BLOCK-iT™-DEST vector with MCF10A cells transfected with a pLenti6/BLOCK-iT™-DEST vector containing TRIM29 shRNA targeting nucleotides 1265–1285 of the TRIM29 open reading frame (ORF, NM_012101). Transcriptional profiling of human breast cancer cells MCF7 comparing control MCF7 cells transfected with a pLenti6.2/N-LumioTM/V5-DEST vector with MCF7 cells transfected with a pLenti6.2/N-LumioTM/V5-DEST vector containing TRIM29 full-length cDNA (ORF, NM_012101). Two-condition experiment, MCF10A-vector control vs. MCF10A-TRIM29 shRNA cells; MCF7-vector control vs. MCF7-TRIM29 cells.
Project description:Transcriptional profiling of human normal-like breast cells MCF10A comparing control MCF10A cells transfected with a pLenti6/BLOCK-iT™-DEST vector with MCF10A cells transfected with a pLenti6/BLOCK-iT™-DEST vector containing TRIM29 shRNA targeting nucleotides 1265–1285 of the TRIM29 open reading frame (ORF, NM_012101). Transcriptional profiling of human breast cancer cells MCF7 comparing control MCF7 cells transfected with a pLenti6.2/N-LumioTM/V5-DEST vector with MCF7 cells transfected with a pLenti6.2/N-LumioTM/V5-DEST vector containing TRIM29 full-length cDNA (ORF, NM_012101). Overall design: Two-condition experiment, MCF10A-vector control vs. MCF10A-TRIM29 shRNA cells; MCF7-vector control vs. MCF7-TRIM29 cells.
Project description:Transgelin was the top-ranked marker of metastatic potential identified in the comparison of node-positive colorectal cancer (CRC) versus node-negative CRC in our previous study. Transgelin is localized in the nucleus of cultured CRC cells and microRNA-mediated knockdown of TAGLN (the gene encoding transgelin) expression modulates the expression of genes involved in the epithelial-to-mesenchymal transition. We performed gene expression profiling on control and transgelin-overexpressing RKO cells using Affymetrix microarray technology. The plasmid carrying TAGLN was generated using the pcDNA6.2/EmGFP-Bsd/V5-DEST vector (Invitrogen, Carlsbad, CA) and the pDONR221-TAGLN-mut plasmid from a previous study by an LR recombination reaction (http://www.invitrogen.com). After lipofectamine-mediated transfection of the TAGLN-carrying plasmid or the vector-only control plasmid, stable transfectants were selected and cultured in medium containing 25 μg/ml blasticidin followed by RNA extraction and hybridization on Affymetrix microarrays. Six samples were obtained from three independent experiments (technical replicates).
Project description:Our study represents a detailed analysis of MCF10A and MCF7 transcriptomes, with biologic replicates, generated by RNA-seq technology Overall design: Expression profiling of cell lines MCF10A and MCF7 that were untreated or treated with 1mM octyl-2HG, 1 mM control compound, transfected with empty vector or ADHFE1-overexpression construct.
Project description:For this study we selected a gene, α-synuclein (SNCA), that is consistently under-expressed in MCF7 cells and breast tumors. Following transfection with an SNCA expression construct, two stable MCF7 clones (named MCF7-SNCA #1 and 2) were selected and examined for expression differences relative to the parental MCF7 cells. MCF7 cells were transfected with an expression vector containing the full-length SNCA sequence. After selection with blasticidin, two different clones were isolated and examined for expression differences relative to the parental MCF7 cells.
Project description:Analysis of differentially expressed genes in MCF7 cancer cells transfected with an expression vector containing the ORF of NIK, a shRNA of NIK and a control shRNA. Transient transfections were performed in triplicates . We use micorarrays to elucidate the machanisms by which NIK regulates stem cells biology Overall design: Three groups were analyzed in triplicate each. The First group was MCF7 group· transfected with an expression vector that overexpress NIK, other group was MCF7 cells transfected with a shRNA to inhibit NIK and the last group was transfected with a shRNA to inhibit luciferase expression.
Project description:The aim was to identify gene expression changes upon expression of KIAA1199 in a colon cancer cell line. Inducible expression of KIAA1199A was achieved with a two-step procedure. First, SW480 cells were transfected with the pcDNA6TR vector (Invitrogen) and the tetracycline repressor-expressing cells selected with 7 μg/ml blasticidin S (InvivoGen). The blasticidin-resistant cells were then transfected with the pT-Rex-DEST30-KIAA1199 construct (see below) and selected with 0.4 mg/ml G418. The growth medium used for these cells was supplemented with 10% Tet-system-approved fetal calf serum (Biochrom).
Project description:These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. MCF10A is a normal-like mammary epithelial cell line and MCF7 is a transformed estrogen responsive breast cancer cell line derived from a metastatic site; both are commonly used in models of breast cancer progression. Analysis revealed a set of genes related to repression of WNT signalling that were both up-regulated in MCF7 and located in genomic regions that had transitioned from closed to open structure in MCF7. RNA-seq of MCF10A and MCF7 cells. 3 replicates each. Sequencing was strand-specific and conducted on ribo-depleted RNA.
Project description:The molecular signature at histone H3K4 involved in epigenetic regulation of normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology. This study examines the dynamic distribution of H3K4me3 and H3K4ac histone modification associated with active chromatin to provide an understanding of the changes in epigenetic regulation associated with the unique breast cancer subtypes. H3K4me3 and H3K4ac histone modification study in normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology
Project description:Gene expression for NCI-H1299 cell line transfected with human DENND2D and vector (pcDNA3.1/V5-His TOPO TA vector) respectively. Overall design: The microarray experiment was designed to perform four replicates for each H1299-DENND2D and H1299-vector sample. cRNA used in replication 1 and 2 was from the same label reaction to perform the hybridization replicates.
Project description:Amplificaition of HOXD9 and HOXD13 genes was found in MWCNTs induced carcinogencity. By overexpression or silence of of HOXD9 and HOXD13 gene may alter tumorigenicity. To investigate the realted signaling pathways invovled in HOXD regulated tumorigencity, we analyzed the gene expression profile of the HOXD9 or HOXD13 overexpression HEK293 cells, which compared to vehicle expressing cells HEK293 cells was transfected with HA-tag-HOXD9 and V5-tag HOXD13 vector, and further selected by G418. Three independnent clones and mix clones of each genes were selected, and compared to corresponding tag control cell. (HA-HOXD9-mix, a, b, c v.s HA-MOCK-1, 2, 3) (V5-HOXD13-mix, a, b, c v.s V5-MOCK-1, 2, 3)