Proteomics 2D gel ISA file (Metadata)

<p>The file contains (i) general information on the experiment and the protocols related to 2d gel proteomics on the “i_Organism” tab, (ii) information on each animal in the “s_Organism” tab, (iii) information on the samples that were measured in the “s_DP_Prot” tab, (iv) the links between the metadata and the image files given in the Data records 17 in the “a_DP_Prot” tab, (v) information on the data that was normalized in the “s_PR_Prot” tab, (vi) the links between the metadata and the normalized matrix given in the file 2D-PAGE data - normalized matrix</p

2D-PAGE data - normalized matrix

<p>Normalilzed matrix of protein measurements in lung by 2d-gel analysis.</p

Proteomics reverse phase protein array data

<p>For the correction of anti-species secondary antibody staining, arrays were assayed in the absence of primary antibodies. For the measurement of spotted protein, one blank chip (i.e., without antibody incubation) was stained with SYPROÒRuby. Scanned images were analyzed using ZeptoVIEW 3.1 software (Bayer Technology Services GmbH). Normalized fluorescence intensities (NFIs) for each sample and protein target were calculated as reference fluorescence intensities of primary antibody stained arrays (RFIprimary) corrected for secondary antibody staining (RFIsecondary), as well as relative spotted protein concentration (RFIprotein), determined by (RFIprimary − RFIsecondary) / RFIprotein, using ZeptoVIEW 3.1 software. NFI values were used for subsequent analysis.</p> <p>A series of bovine serum albumin references were spotted on each array. Each sample underwent serial dilution (100%, 75%, 50%, and 25%) to assess linearity. Prior to RPA analysis, all antibodies were validated by western blotting to assess their specificity.</p

Proteomics 2D gel images

<p>images of the 2d gels for lung proteomics analysis</p

Proteomics reverse phase protein array ISA file (Metadata)

<p>The file contains (i) general information on the experiment and the protocols related to reverse phase protein array proteomics on the “i_Organism” tab, (ii) information on each animal in the “s_Organism” tab, (iii) information on the samples that were measured in the “s_DP_Prot” tab, (iv) the links between the metadata and the data given in the Proteomics reverse phase protein array data file.</p

Effects of cigarette smoke, cessation and switching to a candidate modified risk tobacco product on the liver in <i>Apoe</i>^−/− mice – a systems toxicology analysis

<p>The liver is one of the most important organs involved in elimination of xenobiotic and potentially toxic substances. Cigarette smoke (CS) contains more than 7000 chemicals, including those that exert biological effects and cause smoking-related diseases. Though CS is not directly hepatotoxic, a growing body of evidence suggests that it may exacerbate pre-existing chronic liver disease. In this study, we integrated toxicological endpoints with molecular measurements and computational analyses to investigate effects of exposures on the livers of <i>Apoe^−/−</i>mice. Mice were exposed to 3R4F reference CS, to an aerosol from the Tobacco Heating System (THS) 2.2, a candidate modified risk tobacco product (MRTP) or to filtered air (Sham) for up to 8 months. THS2.2 takes advantage of a “heat-not-burn” technology that, by heating tobacco, avoids pyrogenesis and pyrosynthesis. After CS exposure for 2 months, some groups were either switched to the MRTP or filtered air. While no group showed clear signs of hepatotoxicity, integrative analysis of proteomics and transcriptomics data showed a CS-dependent impairment of specific biological networks. These networks included lipid and xenobiotic metabolism and iron homeostasis that likely contributed synergistically to exacerbating oxidative stress. In contrast, most proteomic and transcriptomic changes were lower in mice exposed to THS2.2 and in the cessation and switching groups compared to the CS group. Our findings elucidate the complex biological responses of the liver to CS exposure. Furthermore, they provide evidence that THS2.2 aerosol has reduced biological effects, as compared with CS, on the livers of <i>Apoe^−/−</i>mice.</p

Moribund and dead animals and missing values

<p>The file gives the description of moribund or dead animals which have been replaced by reserve animals in the study, as well as in the “Missing_Values” tab the samples for which there is no available measurement in a particular endpoint with the associated reason.</p

Study overview file

<p>The file gives for each sample the animal<br>(with its coded animal number, CAN), the exposure group to which it belongs, the test or endpoint that was measured, and the name of the file where the data is given.</p