LLDPE-condition RNA-seq and gene annotation resources for Brucella intermedia isolate X

Dataset: LLDPE-condition RNA-seq (Illumina) + reference annotation + derived TPM tables Associated preprint-------------------This dataset accompanies:https://www.biorxiv.org/content/10.1101/2025.11.09.687417v1 Overview--------This deposit contains (i) raw Illumina paired-end RNA-seq FASTQ files for three LLDPE-grown transcriptome replicates,(ii) the reference genome and annotation used for read counting, and (iii) derived gene-level count and TPM summarytables used to generate the manuscript figures (Figure 4 and associated SI analyses). Sample mapping (manuscript labels ↔ raw data folders - zipped.)-----------------------------------------------------LLDPE-1 = sample B_7 (raw FASTQ folder: B_7-ds.383ecebce4294423864ff9545274b031/)LLDPE-2 = sample B_8 (raw FASTQ folder: B_8-ds.b5d54cd4deee491d87ce05e7eee1bc31/)LLDPE-3 = sample B_6 (raw FASTQ folder: B_6-ds.5d62615b97e346f0989ee878c13fdb13/) Raw read files (FASTQ)----------------------Each raw-data folder contains gzipped paired-end FASTQ files: *_R1_*.fastq.gz (Read 1) *_R2_*.fastq.gz (Read 2) Reference genome and annotation (used for counting)---------------------------------------------------X_genome.fna - Reference genome FASTA used for alignment and quantification. X_genome.gff - Reference genome annotation (GFF3). Gene-level read counts were summarized at CDS features grouped by locus_tag. Derived quantification outputs------------------------------LLDPE_B6B8_q20.featureCounts.txt - Gene-level read counts from featureCounts for the three LLDPE replicates using MAPQ>=20 filtered alignments. - Includes gene length (bp) for TPM calculation. LLDPE_B6B8_q20.featureCounts.txt.summary - featureCounts assignment summary for each replicate. LLDPE_B6B8_q20.all_plastic-degrader_candidates_ranked_with_stats_TPM.csv - TPM-based expression table for the 42 plastic-degradation candidate genes (candidate panel). - Includes per-replicate TPM values (LLDPE-1/2/3) and summary statistics used for plotting. LLDPE_B6B8_q20.biofilm_candidates_TPM.csv - TPM-based expression table for biofilm-associated candidate genes (used for supplementary analyses). Notes on processing (high-level)--------------------------------Reads were adapter/quality-trimmed and aligned to the reference genome. To focus on high-confidence reference-derivedsignal, downstream quantification used alignments filtered at mapping quality MAPQ>=20 prior to featureCounts.Expression values are reported as TPM (transcripts per million; length- and library-size normalized). Contact-------For questions about file contents or usage, please contact the corresponding author(s) of the manuscript.