Open Access Research

Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression

Jennifer Beane12*, Paola Sebastiani3, Gang Liu2, Jerome S Brody2, Marc E Lenburg24 and Avrum Spira12

Author Affiliations

1 Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA

2 The Pulmonary Center, Boston University Medical Center, Albany Street, Boston, MA 02118, USA

3 School of Public Health, Boston University, Albany Street, Boston, MA 02118, USA

4 Department of Genetics and Genomics, Boston University, Albany Street, Boston, MA 02118, USA

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Genome Biology 2007, 8:R201  doi:10.1186/gb-2007-8-9-r201

Published: 25 September 2007

Additional files

Additional data file 1:

For each gene the following information is given: the Affymetrix identification, the HUGO gene symbol, the direction of the change (up- or down-regulated in current smokers with respect to never smokers), the gene classification based on behavior of former smokers, and the percent reversibility.

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Open Data

Additional data file 2:

For each dataset the following information is included: GEO series identification, microarray platform, cell type, where the cells were obtained, cell donor information (if applicable), number of samples, experiment type, exposure, experiment description, data preprocessing, and PUBMED identification (if applicable).

Format: XLS Size: 19KB Download file

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Open Data

Additional data file 3:

Average Pearson correlations between seven pairs of replicate samples where probeset gene expression values were determined using Microarray Suite 5.0 (MAS 5.0), log-transformed data from Microarray Suite 5.0 (Log2 MAS 5.0), and RMA. The average, standard deviation, and median of the correlation coefficients are shown.

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Additional data file 4:

This file explains how the samples used in the present study overlap with previous publications. GEO identifications are provided for each sample for the present study and for the previously published studies (each study used different data preprocessing). GEO identification 1 refers to the study published in [15] (15210990), GEO identification 2 refers to the study published in [27] (17334370), and GEO identification 3 refers to the present study. The study published in [48] (15608264) did not have an accompanying GEO submission.

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Open Data

Additional data file 5:

Primer sequences for the four candidate genes (ALDH3A1, CEACAM5, CYP1B1, and NQO1) designed with PRIMER EXPRESS software (Applied Biosystems), and the primer sequences of the housekeeping gene GAPDH adopted from Vandesompele et al. [59].

Format: XLS Size: 15KB Download file

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Open Data