{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alex Mullins"],"organism":["Burkholderia gladioli"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13521"],"description":["The experiment was intended to understand the influence of growth media on the expression of biosynthetic gene clusters responsible for natural product production."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Growth conditions varied depending on species/strain and experimental variables - see publication for details","Library 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Burkholderia gladioli"],"pubmed_authors":["Alex Mullins"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of Burkholderia gladioli and Burkholderia ambifaria strains on TSB, BSMG, and PEM growth media","description":"The experiment was intended to understand the influence of growth media on the expression of biosynthetic gene clusters responsible for natural product production.","dates":{"release":"2026-06-30T00:00:00Z","modification":"2026-06-30T01:00:54.571Z","creation":"2023-11-07T15:14:43.108Z"},"accession":"E-MTAB-13521","cross_references":{"ENA":["ERP153256"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}