{"database": "metadata", "table": "run_metadata", "rows": [[19182, "ERR14086560", "ERX13488934", "ERS21188924", "ERP165174", "PRJEB81327", "A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite  Ichthyophthirius multifiliis", "420c6801-49a8-433c-9e91-52e1fc6cc95a", "Other", "Ichthyophthirius multifiliis  the causative agent of white spot disease  is associated with high mortality  morbidity  and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity  infecting nearly all freshwater fish species  with severe cases reported in rainbow trout Oncorhynchus mykiss  common carp Cyprinus carpio  and channel catfish Ictalurus punctatus. In contrast  zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood  though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using  transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis  and gill samples were collected at 2  24  48  and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response  peaking at 24 hpi with 1 231 differentially expressed DE genes  before returning to normal levels. In contrast  rainbow trout exhibited a much weaker response  with only 28 DE genes at 24 hpi  and the response normalized by 72 hpi. In zebrafish  DE genes were associated with six immune related pathways  however all DE genes were significantly downregulated  suggesting that the zebrafish may have cleared the infection early  negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish  however  in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune responses  such as Cxcl8a  Cxcl13  and Cxcl11  were upregulated  highlighting the role of immune cells in combating I. multifiliis. Overall  this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h F3 T2", "ZF Con 72h F3 T2", "SAMEA116144983", "CEH,Center for Evolutionary Hologenomics", "ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F3 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F3 T2|scientific name:Danio rerio|status:control|tissue type:gill", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:222 27807", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_F3_T2.pair1.truncated ZF_Con_72h_F3_T2.pair2.truncated", "fastq fastq", 13158999675.0, 43988093.0, "ena RUN TAB 19 12 2024 10:07:07:223 27808", "0:149.57 1:149.57", "A:3612242281;C:2968585225;G:2988176368;T:3589814432;N:181369", 149, 149, null, null, 3612242281, 2968585225, 2988176368, 3589814432, 181369, "ERX13488934", "ERS21188924", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["19182"], "units": {}, "query_ms": 11.463773989817128}