Smoke chemistry

<p>The file contains the concentrations of 58 harmful and potentially harmful constituents measured in aerosols from 3R4F and the pMRTP.</p

Supplementary Table 1. Results of proteomics data including phosphoproteomics and cytokine level measurements for primary normal human bronchial epithelial cells (NHBE) and normal rat bronchial epithelial cells (NRBE) cells exposed to 52 stimuli.

<p>Supplementary Table 1. Results of proteomics data including phosphoproteomics and cytokine level measurements for primary normal human bronchial epithelial cells (NHBE) and normal rat bronchial epithelial cells (NRBE) cells exposed to 52 stimuli.</p> <p>The file contains the median of bead fluorescence intensities measured for each protein in every sample (cell lysate and corresponding supernatant for phosphoproteins and cytokines, respectively). For each stimulus, sample replicates have been extracted from 3 independent wells. The results are reported for (a) 19 phosphoproteins, with in addition the measurements for 2 control beads (Control A: Phycoerythrin-coated beads used as positive control bead; Control B: BSA-coated beads devoid of antibody used as negative control bead), and for the actin; (b) 22 cytokines.</p

Supplementary Table 2. Results of phosphoprotein measurements in primary normal human bronchial epithelial cells (NHBE) and normal rat bronchial epithelial cells (NRBE) using antibody-bead based assays for the experimental screening of 270 stimuli.

<p>Supplementary Table 2. Results of phosphoprotein measurements in primary normal human bronchial epithelial cells (NHBE) and normal rat bronchial epithelial cells (NRBE) using antibody-bead based assays for the experimental screening of 270 stimuli.</p> <p>After an exposure of 5 minutes to each stimulus, cells were lysed and used to measure phosphoproteins. Data were analyzed and a final selection of 52 stimuli used for the main experiment was performed (Data deposited in the figshare public repository).</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

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The file gives the description of moribund or dead animals which have been replaced by reserve animals in the study, as well as in the “Missing_Values” tab the samples for which there is no available measurement in a particular endpoint with the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

Original networks, NVC networks and COPD data sets used in: Enhancement of COPD biological networks using a web-based collaboration interface

<p>Original networks, NVC networks and their descriptions.<br>The file contains the names of the original networks (as they were published), agglomerated NVC networks (as presented on the Bionet website), and network descriptions. The 15 networks that were discussed during jamboree are indicated by “X” in the column Discussed in Jamboree.</p> <p>COPD data sets, their descriptions, and the comparisons used to build the COPD models during Phase 1.<br>Reverse causal reasoning was performed using COPD and emphysema data sets from lung, small airway, and alveolar macrophages of early COPD patients and healthy smokers. Data Sets, the Gene Expression Omnibus (GEO) used to build the COPD networks. SCs, state changes defined using differentially expressed genes that meet the following criteria: FDR adjusted p<0.05, fold change ≥1.3, and minimum expression of 100 (for Affy platforms). HYPs, mechanisms or hypotheses predicted from the SCs and the Selventa Knowledgebase [1] with the following cutoffs: richness p<0.1, concordance p<0.1.</p> <p>Early COPD was defined as Global Initiative for Chronic Obstructive Lung Disease (GOLD) stages 1 and 2.<br>The three small airway data sets were merged using ComBat [2] because of the small sample size of early COPD patients within each data set.<br>Lone emphysema is defined in the GSE10006 data set as patients who have normal spirometry but decreased transfer factor and evidence of emphysema on chest computed tomography scans. The lone emphysema data were selected because they might be useful in understanding COPD onset.</p> <p>References<br>1. Catlett NL, Bargnesi AJ, Ungerer S, Seagaran T, Ladd W, Elliston KO, Pratt D: Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. BMC bioinformatics 2013, 14:340.<br>2. Chen C, Grennan K, Badner J, Zhang D, Gershon E, Jin L, Liu C: Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PloS one 2011, 6:e17238.</p> <p> </p