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Gene expression of lung macrophages in mice instilled with Silica, TiO2 or Saline

ABSTRACT: Mice were intranasally instilled at 6 weeks of age with silica, titanium dioxide, or saline control and macrophages were harvested by broncho-alveolar lavage at 14 weeks of age. RNA was isolated using RNeasy Mini kits (Qiagen). Due to low yield of RNA, mRNA was amplifed by RiboAmp kits (Arcturus) and resulting aRNA was indirectly labeled with Alexa-Fluor 647 dye (Molecular Probes). This was hybridized against Universal Mouse Reference RNA (Stratagene) which was indirectly labeled with Alexa-Fluor 555 dye (Molecular Probes). Slides were printed in house using PCR product cDNA targets on GAPS slides (Corning). Slides were scanned with an Axon GenePix 4000B scanner and data was analyzed using GenePix Pro 4.0 software and Iobion GeneTraffic Duo software. Data was normalized to a total 1:1 ratio of read to green dye. Keywords: parallel sample

ORGANISM(S): Mus musculus

PROVIDER: GSE2279 | GEO | 2005/02/18

SECONDARY ACCESSION(S): PRJNA91451

REPOSITORIES: GEO

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Project description:Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. Genes regulated by sigma(M) have a characteristic pattern of induction in response to cell envelope-acting antibiotics as evidenced by hierarchical clustering analysis. sigma(M) also contributes to the expression of the Spx transcription factor and thereby indirectly regulates genes of the Spx regulon. Cell envelope stress responses also include regulons controlled by sigma(W), sigma(B) and several two-component regulatory systems (e.g. LiaRS, YycFG, BceRS). Activation of the sigma(M) regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification. WT (-van) vs. WT (+van), sigM (-van) vs. sigM (+van), WT (-van) vs. sigM (-van), WT (+van) vs. sigM (+van), WT (-van) vs. spx (-van), WT (+van) vs. spx (+van). Each experiment was conducted at least twice using two independent total RNA preparations. For vancomycin untreated and treated experiments, untreated samples were labeled with Alexa Fluor 555 and treated samples with Alexa Fluor 647. For WT vs. mutant experiments, wild type was labeled with Alexa Fluor 555 and mutants with Alexa Fluor 647. For dye swap experiment, wild-type was labeled with Alexa Fluor 647 and mutant with Alexa Fluor 555. Bacillus subtilis CU1065, WT (-van) vs. WT (+van), sigM (-van) vs. sigM (+van), WT (-van) vs. sigM (-van), WT (+van) vs. sigM (+van), WT (-van) vs. spx (-van), WT (+van) vs. spx (+van)

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Gene expression of lung macrophages in mice instilled with Silica, TiO2 or Saline

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