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Unknown,Transcriptomics,Genomics,Proteomics

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WT macrophage response to WT L. monocytogenes, with or without CAPE treatment

ABSTRACT: Transcriptional profiling of WT macrophages infected with WT L. monocytogenes for 180 minutes, with or without CAPE treatment Keywords: Drug comparison. Experiment in WT background, with WT bacteria, with or without drug treatment. Multiple biological replicates (see array names), with one replicate per array.

ORGANISM(S): Mus musculus

SUBMITTER: Jess Leber

PROVIDER: E-GEOD-8102 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Distinct TLR- and NLR-mediated transcriptional responses to an intracellular pathogen.

Leber Jess H JH Crimmins Gregory T GT Raghavan Sridharan S Meyer-Morse Nicole P NP Cox Jeffery S JS Portnoy Daniel A DA

PLoS pathogens 20080101 1

How the innate immune system tailors specific responses to diverse microbial infections is not well understood. Cells use a limited number of host receptors and signaling pathways to both discriminate among extracellular and intracellular microbes, and also to generate responses commensurate to each threat. Here, we have addressed these questions by using DNA microarrays to monitor the macrophage transcriptional response to the intracellular bacterial pathogen Listeria monocytogenes. By utilizin ...[more]

PMID: 18193943

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Primary macrophage response to L. monocytogenes and bacteria-derived ligands

Project description:Transcriptional profiling of macrophages (of various genetic backgrounds) infected with L. monocytogenes or transfected with purified ligands Keywords: Timecourse, cell type comparison, bacteria strain comparison, drug comparison, ligand comparison. Timecourse experiment in different genetic backgrounds, with both WT and mutant bacteria, and with different combinations of purified ligands. Multiple biological replicates (see array names), with one replicate per array.

2010-05-27 | E-GEOD-8104 | biostudies-arrayexpress

WT and irf3-/- macrophage response to WT L. monocytogenes

Project description:Transcriptional profiling of WT and irf3-/- macrophages infected with WT L. monocytogenes for 180 minutes Keywords: Cell type comparison. Experiment in different genetic backgrounds, with WT bacteria. Multiple biological replicates (see array names), with one replicate per array.

2010-05-27 | E-GEOD-8101 | biostudies-arrayexpress

WT macrophage response to transfected bacterial ligands

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2010-05-27 | E-GEOD-8103 | biostudies-arrayexpress

WT and myd88-/- macrophage response to WT and hly- L. monocytogenes

Project description:Transcriptional profiling of WT and myd88-/- macrophages infected with WT and hly- L. monocytogenes for 30, 60, 120, or 180 minutes Keywords: Timecourse, cell type comparison, bacteria strain comparison. Timecourse experiment in different genetic backgrounds, with both WT and mutant bacteria. Multiple biological replicates (see array names), with one replicate per array.

2007-12-31 | E-GEOD-8100 | biostudies-arrayexpress

WT macrophage response to WT L. monocytogenes, with or without CAPE treatment

Project description:Transcriptional profiling of WT macrophages infected with WT L. monocytogenes for 180 minutes, with or without CAPE treatment Keywords: Drug comparison.

2008-01-01 | GSE8102 | GEO

Gene expression profiling of caffeic acid phenethyl ester-treated human umbilical vein endothelial cells-2

Project description:Caffeic acid phenethyl ester (CAPE), derived from various plant sources, has been shown to ameliorate ischemia/reperfusion (I/R) injury in vivo, and this has been attributed to its ability to reduce the oxidative stress. Here we investigated the cytoprotection of CAPE against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC) to evaluate potential gene expression involvement. CAPE exhibited dose-dependent cytoprotection of HUVEC that required preincubation. A gene screen with microarrays was performed to identify the potential cytoprotective gene(s) induced by CAPE. Heme oxygenase-1 (HO-1) was highly upregulated by CAPE and this was confirmed with reverse transcriptase polymerase chain reaction (RT-PCR) and western blotting. Keywords: gene expression in HUVEC, CAPE cytoprotective dose response Confluent HUVEC were incubated with cytoprotective dose of CAPE at 5 Âµg/ml or 0.1% DMSO as vehicle control for 6 hrs. Both treatments were done in triplicates. Total RNA was isolated at the end of the treatment and applied to microarray experiments in order to identify transcriptional response of HUVEC to CAPE. Microarray experiments were based on a two-color reference design using human universal reference RNA to compare results bwtween CAPE treatment and vehicle control groups.

2010-05-26 | E-GEOD-10429 | biostudies-arrayexpress

Gene expression profiling of caffeic acid phenethyl ester-treated human umbilical vein endothelial cells-1

Project description:Caffeic acid phenethyl ester (CAPE), derived from various plant sources, has been shown to ameliorate ischemia/reperfusion (I/R) injury in vivo, and this has been attributed to its ability to reduce the oxidative stress. Here we investigated the cytoprotection of CAPE against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC) to evaluate potential gene expression involvement. CAPE exhibited dose-dependent cytoprotection of HUVEC that required preincubation. A gene screen with microarrays was performed to identify the potential cytoprotective gene(s) induced by CAPE. Heme oxygenase-1 (HO-1) was highly upregulated by CAPE and this was confirmed with reverse transcriptase polymerase chain reaction (RT-PCR) and western blotting. Keywords: Gene expression in HUVEC, CAPE cytoprotective dose response Confluent HUVEC were incubated with cytoprotective dose of CAPE at 5 Âµg/ml or 0.1% DMSO as vehicle control for 6 hrs. Both treatments were done in triplicates. Total RNA was isolated at the end of the treatment and applied to microarray experiments in order to identify transcriptional response of HUVEC to CAPE. Microarray experiments were based on a two-color reference design using human universal reference RNA to compare results bwtween CAPE treatment and vehicle control groups.

2010-05-26 | E-GEOD-10413 | biostudies-arrayexpress

Transcriptional profiling of PC-3 human prostate cancer cells in response to caffeic acid phenethyl ester treatment

Project description:PC-3 prostate cancer cells were treated with caffeic acid phenethyl ester (CAPE) or vehicle control for 24 h and 72 h for transcription microarray analysis.

2012-08-22 | E-MTAB-773 | biostudies-arrayexpress

Gene expression profiling of hepatocarcinogenesis initiation in Fischer-344 rats.

Project description:Diethylnitrosamine is used as initiator carcinogen in the modiffied resistan model but is not known its effect on gene expression profile on this stage. In other way, CAPE is compound with anticarcinogenic propertie when is administered 12 h before DEN and with the aim to characterize its effect on gene expression profile when is administered alone and in combination with diethylnitrosamine, these analysis were made. Male Fischer-344 rats were we used 4 animal per each treatment and all treatments are compared with not treated rats. Were identified groups of genes related with Carcinogens metabolism, oxidative stress and cell regulation with important differences between treatments. RT-PCR, enzyme activities, wester blots, metabolism assays were performed to validate these results.

2009-06-30 | E-GEOD-12030 | biostudies-arrayexpress

Transcription profiling of mouse adult male wild-type liver (M-WT), adult female wild-type liver (F-WT), adult male liver-specific HNF4alpha knockout liver (M-KO) and adult female liver-specific HNF4alpha knockout liver (F-KO) to investigate sex-dependent and HNF4alpha-dependent gene expression

Project description:A series of dual-channel gene expression profiles obtained using Rosetta/Agilent Whole Mouse Genome oligonucleotide microarrays, 4 x 44K format, was used to identify sex-dependent and HNF4alpha-dependent differences in gene expression in adult mouse liver. This series is comprised of four sex-genotype combinations: adult male wild-type liver (M-WT), adult female wild-type liver (F-WT), adult male liver-specific HNF4alpha knockout liver (M-KO) and adult female liver-specific HNF4alpha knockout liver (F-KO). Four pools, each comprised of 4 randomly selected individual liver RNAs, were prepared for each sex-genotype combination. The pools were paired randomly to generate 4 separate experimental comparisons: M-WT:F-WT (first array comparison), M-WT:M-KO (second array comparison), F-WT:F-KO (third array comparison), and M-KO:F-KO (fourth array comparison). A total of 4994 HNF4alpha-dependent genes were identified, of which ~1000 fewer genes responded to the loss of HNF4alpha in female liver as compared to male liver. Moreover, 90% of the genes showing sex-specific expression in the liver were shown to lose sex specificity in HNF4alpha-deficient liver. Experiment Overall Design: An Alexa555-labeled cDNA sample is co-hybridized with an Alexa647-labeled cDNA sample. The samples are then dye-swapped and compared again on a second microarray chip. Together, these two mixed cDNA samples are considered a fluorescent reverse pair (dye swap). Similarly, a second fluorescent reverse pair is generated and the two pairs are averaged. The normalized expression ratio for each array is reported along with the two separate intensities. In this way, dye swaps were carried out for each of the four experimental comparisons. Thus, four microarrays, one for each mixed cDNA sample, were hybridized for each of the four fluorescent reverse pairs, giving a total of 16 microarrays.

2008-04-04 | E-GEOD-10390 | biostudies-arrayexpress

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