Sequencing data for: Differentially Expressed Infection-Associated Genes in a Shewanella algae isolate From a Deceased Northern Bottlenose Whale

This dataset contains sequencing data generated as part of a study investigating the transcriptional response of a Shewanella algae isolate recovered from the brain tissue of a deceased northern bottlenose whale (Hyperoodon ampullatus) to exposure to host-derived brain homogenate. The dataset comprises basecalled Oxford Nanopore sequencing reads from eight direct cDNA RNA-sequencing samples, basecalled Oxford Nanopore whole-genome sequencing reads from the S. algae isolate, and a processed zero-radius operational taxonomic unit (zOTU) sequence file generated during the initial 16S rRNA gene-based taxonomic identification of bacterial isolates. The direct cDNA RNA-sequencing dataset consists of eight biological samples representing two culture conditions: cultivation in tryptic soy broth (TSB) and cultivation in TSB supplemented with 5% (v/v) brain homogenate (BH), with four biological replicates per condition. RNA was rRNA depleted and poly(A)-tailed prior to library preparation. cDNA synthesis was performed using the Oxford Nanopore Technologies Direct cDNA Sequencing Kit (SQK-DCS109) with SuperScript IV Reverse Transcriptase. Libraries were prepared using native barcoding and the Ligation Sequencing Kit (SQK-LSK114.24) and sequenced on a PromethION R10.4.1 flow cell. Sequencing reads were live basecalled in super-accuracy mode using MinKNOW. Reads were required to contain barcodes at both ends. The whole-genome sequencing dataset contains raw Oxford Nanopore reads generated from the S. algae isolate. Genomic DNA was extracted using the DNeasy PowerLyzer PowerSoil Kit and sequenced using the Oxford Nanopore Technologies Ligation Sequencing Kit (SQK-LSK110) on a MinION R9.4.1 flow cell. Sequencing reads were live basecalled using Guppy v6.3.9 in MinKNOW v5.3.1. The zOTU file contains processed representative sequences generated from 16S rRNA gene amplicon sequencing and used during the initial taxonomic characterization of bacterial isolates.