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Human tumor cell lines treated with 5AZA-dC vs control untreated cells.

ABSTRACT: Human tumor cell lines treated with 5AZA-dC vs control untreated cells.

PROVIDER: PRJNA525694 | ENA |

REPOSITORIES: ENA

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Human tumor cell lines treated with 5AZA-dC vs control untreated cells.

Project description:Equal amounts of test and reference cDNA Cy-labeled mRNA targets were competitively hybridized against a customized cDNA platform with 4,608 ORESTES (open reading frame expressed sequences tags) representing human genes. With this microarray experiment, we found that N-Myc downstream-regulated gene 4 (NDRG4) is silenced in tumor cells and acts as a mechanistic biomarker of metastasis in ductal invasive breast tumors. While aberrant NDRG4 silencing, by DNA hypermethylation, is significantly associated with the development of metastatic disease, downregulation of NDRG4 transcription and protein expression is functionally associated with enhanced lymph node adhesion and cell mobility. Based on following functional assays, we show that silencing of NDRG4 modulates integrin signaling by assembling β1-integrins into large punctate clusters at the leading edge of tumor cells to promote an “adhesive switch,” decreasing cell adhesion to fibronectin and increasing cell adhesion and migration towards vitronectin, an important component of human lymph nodes.

2019-04-17 | GSE127885 | GEO

S. coelicolor, control (untreated) vs ciprofloxacin-treated

Project description:S. coelicolor, control (untreated) vs ciprofloxacin-treated

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S. coelicolor, Control (untreated) Vs Ciprofloxacin treated

Project description:Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells. Two-condition experiment, Control Vs CIP treatment. Biological replicates: 3 control, One dye swap replicate.

2014-01-01 | GSE49788 | GEO

S. coelicolor, control (untreated) vs ciprofloxacin-treated

Project description:Transcriptional profiling of S. coelicolor cells treated with sub-inhibitory or inhibitory concentrations of ciprofloxacin in comparision to untreated control when cultured in R5 media. Two-condition experiment, Control Vs CIP treatment.

2019-06-01 | GSE115753 | GEO

E.coli DH5alpha cells: reuterin-treated vs. untreated control cells

Project description:Transcriptional profiling of E. coli DH5alpha cells comparing control untreated cells with cells exposed to sublethal concentrations of reuterin (3-hydroxypropionaldehyde).

2010-01-07 | GSE19760 | GEO

DNA methyltransferase inhibitor 5-aza-dC-treated prostate cancer cell lines

Project description:This microarray dataset accompanies the publication by Kim et al, "The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancer". The dataset comprises four prostate cancer cell lines treated with the DNA methyltransferase inhibitor 5-aza-dC. For each cell line, gene expression in treated (channel 2; Cy5) and untreated (channel 1; Cy3) cells is directly compared by hybridization to the same DNA microarray. Further details on the treatment conditions are provided in the manuscript. A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. Keywords: compound_treatment_design

2006-01-25 | GSE4089 | GEO

Analysis of normal lung cells treated with 5-aza-dC to induce DNA demethylation

Project description:Analysis of 2 cultured normal lung cell lines, Normal Human Bronchial Epithelial (NHBE) and Human Small Airway Epithelial (SAEC) cells (Lonza, Walkersville, MD), following treatment with 5-aza-dC to induce DNA demethylation. These results provide insight into the role of epigenetic alterations, specifically demethylation, in differential gene expression in various lung neoplasms. Two normal lung cell lines, NHBE and SAEC, were treated with 5uM 5-aza deoxycytidine for 72 hours and Trichostatin A for 24 hours prior to harvesting total RNA for expression array analysis using the Affymetrix Human Genome U133 Plus 2.0 expression platform. Signal intensity and statistical significance was established for each transcript using dChip version 2005. Two-fold increase based on the 90% confidence interval of the result and expression minus baseline >50 was used as the statistical cutoff value after 5Aza-dC and/or TSA treatment to identify upregulated candidate genes.

2010-10-07 | E-GEOD-18454 | biostudies-arrayexpress

Pseudomonas putida KT2440 : Control vs. recG gene mutant with untreated or paraquat (PQ) treated

Project description:Transcriptional profiling of P. putida KT2440 cells comparing control untreated wild type cells with untreated recG gene mutant cells or PQ treated recG gene mutant cells

2011-12-15 | GSE34410 | GEO

Untreated vs. QR-110 treated retinal organoids

Project description:Untreated vs. QR-110 treated retinal organoids

| PRJNA480264 | ENA

RNAseq of follicular lymphoma patient samples treated with anti-IgM, DC-SIGN or an isotype control

Project description:Here we investigate the relevance of the microenvironment in follicular lymphoma by studying the effect of the lectin DC-SIGN, expressed by macrophages on B-cell receptor activation. We compare the effect of DC-SIGN and anti-IgM stimulation on FL by treating 3 FL samples with 20 μg/ml of goat F(ab’)2 anti-IgM, 20 μg/ml of DC-SIGN-Fc or left untreated for 4 hours at 37°C. Total RNA was extracted using an RNeasy mini kit (Qiagen) and polyA libraries were 75bp PE sequenced on a HiSeq4000 (Ilumina). After gene expression profiling analysis we found that, although DC-SIGN-Fc appears to elicit a weaker transcriptional response than anti-IgM, the responses are closely related and encompass a wide range of canonical BCR response pathways.

2020-01-31 | E-MTAB-8708 | biostudies-arrayexpress

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