Gene expression analysis of alveolar macrophages tolerized to ozone

In this study, we examined the effect of repeated exposure to the air pollutant ozone (O3) on the transcriptome of alveolar macrophages (AMs). Using flow cytometry, we isolated purified AMs from the lungs of female C57BL6/NJ mice exposed to filtered air or 0.8 ppm O3 for four days and then collected 2 days later, with six mice per group. RNA was isolated from AMs and then subjected to RNA-seq analysis. We performed differential gene expression analysis followed by gene ontology enrichment analysis of differentially expressed genes., Alveolar macrophages were isolated from mouse whole lung tissue using flow cytometry. Total RNA was extracted from two batches of flow-sorted AMs using QIAGEN RNAeasy kits per the manufacturer’s instructions. RNA integrity was analyzed using an Agilent Bioanalyzer. RIN values ranged from 8.9-9.7, indicating intact RNA. PolyA+ RNA libraries were prepared with the Roche Kapa mRNA stranded library preparation kit as per the manufacturer's instructions. Paired-end sequencing (50 cycles) was performed on an Illumina NovaSeq SP to a depth of >55M read pairs per sample by the UNC High-Throughput Sequencing Facility. 
Raw reads were trimmed and filtered of adapter contamination using cutadapt (Martin, 2011), and further filtered such that at least 90% of bases had a quality score of at least 20 using fastx_toolkit v0.0.14. Reads were then aligned to the reference mouse genome (mm10) (Supplementary Table 3) and GENCODE vM25 transcript annotations using STAR v2.7.7a (Dobin et al., 2013), ..., , # Gene expression analysis of alveolar macrophages tolerized to ozone

[https://doi.org/10.5061/dryad.pc866t1x9](https://doi.org/10.5061/dryad.pc866t1x9)

The datasets here correspond to supplementary tables 2-5 of a manuscript submission to the journal Toxicological Sciences and include RNA-seq alignments, differential gene expression analysis, and pathway analysis of differentially expressed genes.

## Description of the data and file structure

* Supplementary Table 2 (TableS2) contains RNA-seq alignment results and contains four columns corresponding to the sample name, the number of total reads, the number of uniquely aligned reads, and the percent of mapped reads.
* Supplementary Table 3 (Table S3) contains complete results of differential expression analysis and contains six columns corresponding to gene name, expression level (baseMean, normalized counts), fold change (log2FoldChange, in log2 units), standard error of the fold change (lfcSE), p-value, and adjusted p-value.
* Sup...,