Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene Expression data from mouse bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: lamia Guizani-Tabbane

PROVIDER: E-GEOD-31997 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Leishmania (L.) are obligated intracellular protozoan parasites that develop electively in macrophages. These cells that are acting as a safe shelter for the pathogens but also as their ultimate killer, making them the alpha and the omega during leishmaniasis diseases. Macrophages are able to secrete a remarkably diverse set of regulators known to influence the physiological functions and differentiation of neighboring cells to trigger an adaptive immune response of protective Th1-type cells, whereas parasites have developed a wide range of mechanisms to circumvent the hostâs immune responses. Most of our understanding of this host-parasite conflict, in the context of macrophage invasion by L. major metacyclic promastigotes, has been gleaned from studies investigating the macrophage responses at late and unique time points after infection. To investigate the dynamics of this duel, we have analyzed the transciptomic profile of monocyte-derived human macrophages at different time points during the first 24h upon in vitro infection using high throughput microarray platform. The gene expression profile of 17,838 genes showed high expression variability between the three human donors at different time points post infection. Cross comparison between the three donors allowed the identification of a common set of expressed genes coding for inflammatory and chemotactic molecules, transcription factors, apoptosis inhibition, glucose synthesis and heme metabolism. The findings presented in this work suggest that transcriptome dynamics of macrophages early during the first 24h post infection enable to identify novel key pathways deregulated upon L. major invasion. Our reported set of expressed genes will be useful in future rounds of data mining and functional analyses. In total 27 samples from three different donors were analyzed. For each donor, samples at 0h, 3h, 6h, 12h and 24h of culture were used as controls. For each donor, samples of cells infected with metacyclic Leishmania major parasites at 3h, 6h, 12h and 24h post-infection were analyzed.

Project description:Purification of Nucleosomal DNA T47D-MTVL breast cancer cells carrying one stably integrated copy of the luciferase reporter gene driven by the MMTV promoter (Truss et al., 1995) were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/mL streptomycin. For DNA preparation, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were treated for 5 minutes at 37ºC with 2mL of buffer A (150mM sucrose, 15mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 2mM CaCl2) containing 0,5 mg/mL of lysolecithin. Micrococcal nuclease digestion was performed by adding 2mL of buffer A, supplemented with 720U of MNase (Worthington) for 3 minutes at 37ºC. The reaction was stopped with 40mM EDTA. Cells were scrapped and lysated with 1% SDS, 10mM EDTA and 50mM Tris pH 8.1 buffer, during 10 minutes on ice. Samples were then treated with 0,1mg/mL RNAse A for 30 minutes at 37ºC and 0,1 mg/mL of proteinase K for 1 hour at 45ºC. DNA was purified by phenol/chloroform extractions and ethanol precipitation. The digested DNA was run on 1% agarose gel, and band corresponding to mononucleosomes was gel-extracted. Microarray hybridization Labelling was done using Bioprime genomic labeling kit (Invitrogen, cat.no. 18095-011 and 18095-012) following manufacturers instructions. Briefly, 500 ng isolated nucleosomal DNA or total genomic DNA partially digested with MNase was labeled with either dUTP-Cy5 or dUTP-Cy3 fluorescent mononucleotides (Amersham GE PA55322), respectively. 2 mg of the obtained labeled sample were co-hybridized to the Agilent customized oligo microarray in the presence of 50 mg Human Cot-1 DNA and Agilent oligo aCGH hybridization kit (cat.no. 5188-5220) with includes blocking agents for unspecific hybridization following manufacturers instructions. Hybridization was performed in a rotating oven at 65ºC for 40 hours. Arrays were washed and fluorescent images were acquired using G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings. 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Axon Instruments Inc.). Microarray data was normalized applying a global loess algorithm using a smoothing factor of 0.2 (Yang et al. 2002) obtaining normalized log2[intensity Cy5]/[Intensity Cy3] mean values for each spot on the array.

Dataset Information

Gene Expression data from mouse bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection

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