RNA-seq analysis dataset for Pseudomonas aeruginosa PAO1 37°C vs. 43°C

The data in this item includes raw RNA-sequencing data from post-43°C exposure and during the recovery period to assess transcript-level effect.

Sample preparation: Overall, 18 samples included 3 replicates of Pseudomonas aeruginosa after exposure to 37 °C (control) or 43 °C (heat shock), at 3 time points (T=0hr, T=18hr, and T=54hr). Samples from the T=0 groups are simply labeled “37” or “43”. For RNA sequencing, 2 ug of total RNA was used for the RiboMinus™ Bacteria Transcriptome Isolation Kit (Invitrogen). The library was constructed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions using 30 ng of depleted RNA. The final quality was evaluated by TapeStation High Sensitivity D1000 Assay (Agilent Technologies, CA, USA). Sequencing was performed based on Qubit values and loaded onto an Illumina MiSeq using the MiSeq V2 (50- cycles) Kit (Illumina, CA, USA). Paired-end RNA-seq protocol was used, yielding about 3.4-6.5 million paired-end reads per sample. FastQC (v0.11.2) was used to assess the quality of raw reads.

Analysis: Reads were aligned to Pseudomonas aeruginosa PAO1 strain (assembly GCF_000006765.1 ) using the bowtie2 aligner software (v2.3.2) with default parameters. GTF annotation file for the PAO1 strain was downloaded from NCBIPseudomonas Genome DB ( www.pseudomonas.com). Raw read counts for gene-level features were determined using HTSeq-count with the intersection-strict mode. Differentially expressed genes were determined with the R Bioconductor package DESeq2 (Release 3.14). The p-values were corrected with the Benjamini-Hochberg FDR procedure. Genes with adjusted p-values; 0.05.