biostudies-arrayexpressAlex MullinsBurkholderia gladiolihttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13521The experiment was intended to understand the influence of growth media on the expression of biosynthetic gene clusters responsible for natural product production.biostudies-arrayexpressGrowth Protocol - Growth conditions varied depending on species/strain and experimental variables - see publication for detailsLibrary Construction - Illumina library preparation followed the Illumina Stranded Total RNA Library Prep reference guide. Primer dimers were removed from the pooled library by SPRI bead size selection.Sequencing - Novaseq S1 (200 cycle) sequencing run. Two lanes per sample and data combined.Sample Collection - Starting culture OD of 0.05 (600 nm). 1 ml of liquid culture was harvested for each replicate at the desired optical density. Each 1 ml aliquot was centrifuged, supernatant discarded, and Monarch® DNA/RNA Protection Reagent added prior to snap-freezing in liquid nitrogen.Nucleic Acid Extraction - RNA extracted using Monarch® Total RNA Miniprep Kit (NEB) as described in the NEB Gram-negative bacteria protocol. A final DNase treatment was included using the TURBO DNA-free™ Kit for 1 h.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Count data determined with htseq applying union mode to non-stranded read data, and non-unique reads were assigned to all overlapping features. Log2 fold change and statistical significance determed with DESeq2 v1.32.0 - count data normalised and shrinkage of LFC effect size achieved using apeglm in DESeq2.Sequence Alignment - Reads were trimmed with Trim Galore v0.6.7, quality assessed with FastQC v0.11.9. Processed reads were mapped to references with Bowtie 2 followed by sorting and indexing with samtools v1.7.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of total RNABurkholderia gladioliAlex MullinsfalseRNA-seq of Burkholderia gladioli and Burkholderia ambifaria strains on TSB, BSMG, and PEM growth mediaThe experiment was intended to understand the influence of growth media on the expression of biosynthetic gene clusters responsible for natural product production.2026-06-30T00:00:00Z2026-06-30T01:00:54.571Z2023-11-07T15:14:43.108ZE-MTAB-13521ERP153256EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184