{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Josh Bond"],"instrument_platform":["incubator shaker; spectrophotometer; Cmag measurement system; flow cytometer","thermal cycler; magnetic separation rack; Qubit Fluorometer; Agilent TapeStation 4200","Element AVITI","microcentrifuge; magnetic separation rack; Qubit Flu/spectrophotometer; Agilent TapeStation 4200"],"study_type":["RNA-seq of coding RNA"],"organism":["Magnetospirillum gryphiswaldense"],"species":["Magnetospirillum gryphiswaldense"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17612"],"description":["This experiment investigated the transcriptional response of the magnetotactic bacterium Magnetospirillum gryphiswaldense MSR1 to acute copper stress. Mid-exponential-phase cultures were exposed to five milligrams per litre copper for three hours, with untreated cultures sampled at the start and end of the incubation period. Three biological replicates were analysed for each condition. RNA was extracted, sequenced and subjected to quality assessment before reads were mapped to the MSR1 reference genome and gene counts were analysed using DESeq2. The primary comparison assessed copper-exposed cultures against time-matched controls, while the control time comparison provided context for normal growth-associated transcriptional changes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Magnetospirillum gryphiswaldense (MSR1) was cultivated in Flask Standard Media (FSM) at 30 °C and 150 rpm for 18 h until cultures reached mid-exponential phase, corresponding to an OD565 of approximately 0.15. Pre-exposure samples were collected immediately before treatment and designated as the Time 0 control group. Triplicate cultures were subsequently exposed to CuCl2·2H2O at a final concentration equivalent to 5 ppm Cu, while time-matched control cultures received an equivalent volume of Milli-Q water. Samples were collected after a further 3 h incubation to generate the Time 3 Cu and Time 3 control groups. Three independent biological replicates (BR) were collected for each condition. OD565, cellular magnetic response and cell viability were assessed at each sampli","Library Construction - Bacterial 5S, 16S and 23S rRNA was removed using the QIAseq FastSelect–5S/16S/23S Kit (Qiagen; 335925). Indexed, strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs; E7760L) and NEBNext Multiplex Oligos for Illumina, comprising 96 unique dual-index primer pairs (New England Biolabs; E6440L). PCR amplification was performed using the NEBNext Ultra II Q5 Master Mix, with an initial denaturation at 98 °C for 30 s, followed by 10 cycles of 98 °C for 10 s and 65 °C for 75 s, and a final extension at 65 °C for 5 min. Libraries were quantified using a Qubit Fluorometer with the Qubit dsDNA HS Kit (Thermo Fisher Scientific; Q32854). Library fragment-length distributions were assessed using an A","Sequencing - The pooled libraries were sequenced on the Element Biosciences AVITI platform using the AVITI 2 × 150 Sequencing Kit Cloudbreak FS High Output (Element Biosciences; 860-00013). Sequencing generated at least 10 million 150-bp paired-end reads per biological sample. Demultiplexed sequence data were provided as gzip-compressed FASTQ files, with separate R1 and R2 files generated for sequencing lanes L001 and L002.","Nucleic Acid Extraction - Total RNA was extracted from each MSR1 culture using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol for Gram-negative bacteria. RNA concentrations were measured using a Qubit Fluorometer with the Qubit RNA BR Assay Kit (Thermo Fisher Scientific; Q10211). RNA integrity was assessed using an Agilent TapeStation 4200 with the Agilent RNA ScreenTape Assay Kit (Agilent; 5067-5576 and 5067-5577). Genomic DNA was removed using DNase I treatment (Ambion; AM2222), followed by a 1.8× clean-up using Mag-Bind Total Pure NGS beads (Omega Bio-tek; M1378-00). Samples underwent further quality control to confirm the removal of genomic DNA."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Josh Bond","Tim Overton","Graeme Fox","Alfred Fernandez-Castane","Vesna Najdanovic","Matthew Carlile"],"additional_accession":[]},"is_claimable":false,"name":"Exploring copper toxicity mechanisms in Magnetospirillum gryphiswaldense MSR1 using transcriptomics","description":"This experiment investigated the transcriptional response of the magnetotactic bacterium Magnetospirillum gryphiswaldense MSR1 to acute copper stress. Mid-exponential-phase cultures were exposed to five milligrams per litre copper for three hours, with untreated cultures sampled at the start and end of the incubation period. Three biological replicates were analysed for each condition. RNA was extracted, sequenced and subjected to quality assessment before reads were mapped to the MSR1 reference genome and gene counts were analysed using DESeq2. The primary comparison assessed copper-exposed cultures against time-matched controls, while the control time comparison provided context for normal growth-associated transcriptional changes.","dates":{"release":"2026-09-22T00:00:00Z","modification":"2026-09-22T01:00:38.238Z","creation":"2026-09-08T15:22:15.939Z"},"accession":"E-MTAB-17612","cross_references":{"ENA":["ERP205432"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}