Data of RNA-Seq in Type 2 Alveolar Epithelial Cells Exposed to Diesel Exhaust Particles
Description
This dataset includes the RNA sequencing (RNA-Seq) in MLE-12 type II alveolar epithelial cells (AECII) exposed to diesel exhaust particle (DEP) at 0 (Control) and 50 μg/mL for 6, 16, and 24 hours. The dataset includes the summary of the gene sequenced, differentially expressed genes (DEG), and genes annotated by Disease Ontology (DO), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
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Steps to reproduce
MLE-12 were collected after exposure to DEP at 0 (Control) and 50 μg/mL for 6, 16, and 24 hours. Samples were then homogenized in TRIzol® (Invitrogen, Waltham, MA, USA). The RNA purification was performed by SimpliNano-Biochrom Spectrophotometer (Biochrom, MA, USA). The Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan) was used to examine RNA integrity and degradation. HISAT2 software (v 2.1.0) was used to read pairs from each sample were aligned to the reference genome (Mus musculus, GRCm39). NovaSeq 6000 (Illumina, San Diego, CA, USA) was used for sequencing. Relative Log Expression normalization (RLE) was performed via DESeq2 (v 1.26.0) for gene expression with biological duplicate. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the FDR. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and DEGs enrichment analysis were conducted by clusterProfiler (v 4.4.0)