{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Stephen Dolan"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Aspergillus fumigatus"],"species":["Aspergillus fumigatus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16731"],"description":["This study examines transcriptional changes in Aspergillus fumigatus across different growth environments and in response to bacterial co-culture. A. fumigatus was grown in Sabouraud Dextrose Broth (SDB), synthetic cystic fibrosis medium 2 (SCFM2), and in co-culture with Pseudomonas aeruginosa in SCFM2. Experimental conditions include A. fumigatus monoculture in SDB, monoculture in SCFM2, and co-culture with P. aeruginosa in SCFM2, each performed in biological triplicate. Total RNA was extracted from cultures and rRNA-depleted prior to library preparation and sequencing. This dataset enables analysis of fungal transcriptional adaptation to cystic fibrosis-relevant media and identification of gene expression change associated with bacterial interaction."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Total RNA was DNase treated and ribosomal RNA depleted as described above. Sequencing libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions to generate stranded cDNA libraries suitable for paired-end sequencing.","Sequencing - RNA sequencing was performed on an Illumina NovaSeq 6000 platform (SP flow cell, paired-end 100 bp reads) by the CRUK Cambridge Institute Genomics Core Facility. Raw sequencing reads were quality assessed prior to downstream processing, and multiple forward and reverse read files per sample were concatenated to generate complete FASTQ files for each biological replicate.","Nucleic Acid Extraction - Snap-frozen A. fumigatus mycelia (triplicates per condition) were resuspended in 1 mL PureZOL™ RNA Isolation Reagent and mechanically lysed using a Mini-Beadbeater-16 (4 x 30 sec cycles), cooling on ice between cycles. Total RNA was extracted by chloroform-isopropanol precipitation and resuspended in RNase-free water. RNA (10 µg) was treated with TURBO DNase, ethanol precipitated, and resuspended in RNase-free water. Ribosomal RNA depletion (1 µg input RNA) was performed using the QIAseq FastSelect - rRNA Yeast Kit (Qiagen, #334215).","Sample Collection - A. fumigatus mono-cultures (50 mL) grown in SCFM2 and SDB, and SCFM2 co-cultures with P. aeruginosa were harvested after 32 h of growth (triplicates) by filtering culture contents over a 40 µm cell strainer into a 50 mL conical tube. Retained mycelial biomass was collected from the strainer using a sterile inoculation loop, transferred into 2 mL bead-beating tubes containing 0.1 mm and 1.0 mm Zirconia/Silica beads, and immediately snap-frozen in liquid nitrogen prior to RNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Stephen Dolan"],"additional_accession":[]},"is_claimable":false,"name":"Aspergillus fumigatus transcriptome during growth in SDB, SCFM2, and co-culture with Pseudomonas aeruginosa PA14","description":"This study examines transcriptional changes in Aspergillus fumigatus across different growth environments and in response to bacterial co-culture. A. fumigatus was grown in Sabouraud Dextrose Broth (SDB), synthetic cystic fibrosis medium 2 (SCFM2), and in co-culture with Pseudomonas aeruginosa in SCFM2. Experimental conditions include A. fumigatus monoculture in SDB, monoculture in SCFM2, and co-culture with P. aeruginosa in SCFM2, each performed in biological triplicate. Total RNA was extracted from cultures and rRNA-depleted prior to library preparation and sequencing. This dataset enables analysis of fungal transcriptional adaptation to cystic fibrosis-relevant media and identification of gene expression change associated with bacterial interaction.","dates":{"release":"2026-06-01T00:00:00Z","modification":"2026-06-01T01:00:56.996Z","creation":"2026-03-09T14:42:27.571Z"},"accession":"E-MTAB-16731","cross_references":{"ENA":["ERP190536"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}