biostudies-arrayexpressNaveed AkramOncorhynchus mykisshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16908This experiment investigates how sequential infections with Myxobolus cerebralis and Tetracapsuloides bryosalmonae alter immune responses in rainbow trout. Using RNA-seq of kidney and head cartilage tissues, the study compares transcriptomic changes during single infections and sequential co-infection to determine how combined parasite exposure reshapes host immune pathways and tissue responses.biostudies-arrayexpressSequencing - Sequencing was performed at the NGS unit of the Vienna BioCenter Core Facilities (VBCF, Vienna, Austria) on an Illumina NovaSeq 6000 platform, generating 150 bp paired end reads.Library Construction - For each sample, 500 ng of total RNA were subjected to mRNA enrichment using the Lexogen Poly(A) RNA Selection Kit V1.5 (Lexogen, Vienna, Austria). mRNA-enriched fractions were then used to generate cDNA libraries with the CORALL mRNA-Seq Library Prep Kit (Lexogen), according to the manufacturer’s instructions, yielding a total of 30 libraries (15 kidney and 15 HC). Library size distribution and quality were evaluated using a High Sensitivity D1000 ScreenTape Kit on the Agilent 4200 TapeStation System.Sample Collection - At 90 dpi, fish from each group were euthanized in buffered tricaine methanesulfonate (MS-222) overdose (250–500 mg/L) [81], and death was confirmed before collection of Kidney and Head cartilage sampling and stored at -80°C until further analysis.Nucleic Acid Extraction - Total RNA was isolated from kidney and head cartilage (HC) collected at 90 dp. For each tissue, samples from 15 fish were processed (3 fish per group; 5 experimental groups in total), using a RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. An on-column DNase digestion step was included to remove residual genomic DNA. RNA quantity and purity were assessed with a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Wilmington, USA), and integrity was checked by agarose gel electrophoresis. Only samples with RNA integrity numbers (RIN) ≥ 8.0 were used for library preparation.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Differential gene expression was assessed in CLC Genomics Workbench (Qiagen) using the RNA-Seq differential expression module, which applies negative binomial generalized linear model (multi-factorial design) to read counts and applies TMM (trimmed mean of M-values) normalization.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Parasitic infections, such as those caused by the myxozoans <i>Myxobolus cerebralis</i> and <i>Tetracapsuloides bryosalmonae</i>, pose major threats to wild and farmed salmonids due to severe tissue damage and impairment of the host immune system. While individual infections have been studied, limited information is available on the host response during co-infection. This study investigated the transcriptomic immune response of rainbow trout (<i>Oncorhynchus mykiss</i>) during single and sequential co-infections with <i>M. cerebralis</i> and <i>T. bryosalmonae</i> using RNA-seq. Trout were exposed to single infections (Mc or Tb) followed by co-infections (Mc⁺ or Tb⁺). Fish were sampled at 31 days post-single infection (1 day post-co-infection). RNA from gill and caudal fin (portal of parasite entry) was sequenced, followed by differentially expressed genes (DEGs) identification and GO and KEGG enrichment. In the caudal fin, Mc⁺ (1 day after co-infection with <i>T. bryosalomne</i>) fish showed mild immune activation with <i>C4B</i> upregulation, while Tb⁺ fish exhibited a stronger response involving <i>IFI44, ISG15, RSAD2, and TLR7</i> signaling. In gills, Mc⁺ fish showed moderate cytokine-related gene upregulation, while Tb⁺ (1 day after co-infection with <i>M. cerebralis</i>) fish displayed increased expression of humoral response genes (<i>C3</i>, immunoglobulin pathways) but suppression of genes involved in B cell development. These results indicate that the order of infection shapes the outcome of the host immune response, offering candidate targets at the host-pathogen interface.RNA-seq of coding RNAOncorhynchus mykissTranscriptomic Analysis of the Rainbow Trout Response to Single and Co-Infections with Myxobolus cerebralis and Tetracapsuloides bryosalmonae at Sites of Parasite EntryNaveed AkramNaveed Akram, Reinhard Ertl, Reza Ghanei-Motlagh, Christopher J. Secombes, Mansour El-Matbouli, Astrid S. Holzer, and Mona SalehfalseTissue-Specific Transcriptomic Insights into Myxozoan Infections: Immune and Stress Responses in the Kidney and Head Cartilage of Rainbow TroutThis experiment investigates how sequential infections with Myxobolus cerebralis and Tetracapsuloides bryosalmonae alter immune responses in rainbow trout. Using RNA-seq of kidney and head cartilage tissues, the study compares transcriptomic changes during single infections and sequential co-infection to determine how combined parasite exposure reshapes host immune pathways and tissue responses.2026-04-25T00:00:00Z2026-04-25T01:01:22.332Z2026-04-15T12:27:02.535ZE-MTAB-1690840943072ERP192191EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_000418410.3390/ijms26178148