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66 rows where devstage_curation = "Undetermined" and tissue_curation_coarse = "Respiratory System"

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technology 3

experiment.library_selection 2

devstage_curation_coarse 2

tissue_curation_coarse 1

  • Respiratory System · 66 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

devstage_curation 1

  • Undetermined · 66 ✖
Link 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
19143 19143 ERR14086559 ERX13488933 ERS21188923 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F2 T2 ZF Con 72h F2 T2 SAMEA116144982 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 F2 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:221 27805 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F2_T2.pair1.truncated ZF_Con_72h_F2_T2.pair2.truncated fastq fastq 10806719947.0 36110242.0 ena RUN TAB 19 12 2024 10:07:07:222 27806 0:149.64 1:149.64 A:2965060471;C:2438948465;G:2454160636;T:2948358895;N:191480 149 149     2965060471 2438948465 2454160636 2948358895 191480 ERX13488933 ERS21188923 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19144 19144 ERR14086546 ERX13488920 ERS21188910 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F2 T1 ZF Con 2h F2 T1 SAMEA116144969 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 2h F2 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:206 27779 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F2_T1.pair1.truncated ZF_Con_2h_F2_T1.pair2.truncated fastq fastq 14857999358.0 49760457.0 ena RUN TAB 19 12 2024 10:07:07:207 27780 0:149.30 1:149.29 A:4063197170;C:3359903309;G:3389720319;T:4045034265;N:144295 149 149     4063197170 3359903309 3389720319 4045034265 144295 ERX13488920 ERS21188910 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19145 19145 ERR14086581 ERX13488955 ERS21188945 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F2 T1 ZF Inf 72h F2 T1 SAMEA116145004 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 Inf 72h F2 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F2 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:243 27849 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F2_T1.pair1.truncated ZF_Inf_72h_F2_T1.pair2.truncated fastq fastq 13688478236.0 45721242.0 ena RUN TAB 19 12 2024 10:07:07:244 27850 0:149.69 1:149.69 A:3754535055;C:3089295285;G:3114000296;T:3730455705;N:191895 149 149     3754535055 3089295285 3114000296 3730455705 191895 ERX13488955 ERS21188945 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19146 19146 ERR14086540 ERX13488914 ERS21188904 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F1 T2 ZF Con 24h F1 T2 SAMEA116144963 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 24h F1 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F1 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:199 27767 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F1_T2.pair1.truncated ZF_Con_24h_F1_T2.pair2.truncated fastq fastq 10450579058.0 34942794.0 ena RUN TAB 19 12 2024 10:07:07:200 27768 0:149.54 1:149.54 A:2875878023;C:2351334168;G:2367670600;T:2855687426;N:8841 149 149     2875878023 2351334168 2367670600 2855687426 8841 ERX13488914 ERS21188904 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19147 19147 ERR14086555 ERX13488929 ERS21188919 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F5 T1 ZF Con 48h F5 T1 SAMEA116144978 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 48h F5 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:216 27797 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F5_T1.pair1.truncated ZF_Con_48h_F5_T1.pair2.truncated fastq fastq 12970550968.0 43346641.0 ena RUN TAB 19 12 2024 10:07:07:217 27798 0:149.61 1:149.61 A:3556627514;C:2927267468;G:2954512353;T:3531914408;N:229225 149 149     3556627514 2927267468 2954512353 3531914408 229225 ERX13488929 ERS21188919 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19148 19148 ERR14086548 ERX13488922 ERS21188912 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F3 T1 ZF Con 2h F3 T1 SAMEA116144971 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 2h F3 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F3 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:208 27783 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F3_T1.pair1.truncated ZF_Con_2h_F3_T1.pair2.truncated fastq fastq 9796047940.0 32778493.0 ena RUN TAB 19 12 2024 10:07:07:209 27784 0:149.43 1:149.43 A:2712516144;C:2185151856;G:2203905915;T:2694465752;N:8273 149 149     2712516144 2185151856 2203905915 2694465752 8273 ERX13488922 ERS21188912 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19149 19149 ERR14086576 ERX13488950 ERS21188940 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F2 T1 ZF Inf 48h F2 T1 SAMEA116144999 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 Inf 48h F2 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F2 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27839 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F2_T1.pair1.truncated ZF_Inf_48h_F2_T1.pair2.truncated fastq fastq 10400268770.0 34736762.0 ena RUN TAB 19 12 2024 10:07:07:239 27840 0:149.70 1:149.70 A:2850649951;C:2367895411;G:2362604415;T:2819029152;N:89841 149 149     2850649951 2367895411 2362604415 2819029152 89841 ERX13488950 ERS21188940 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19150 19150 ERR14086580 ERX13488954 ERS21188944 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F5 T2 ZF Inf 48h F5 T2 SAMEA116145003 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 Inf 48h F5 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:242 27847 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F5_T2.pair1.truncated ZF_Inf_48h_F5_T2.pair2.truncated fastq fastq 11541953511.0 38615622.0 ena RUN TAB 19 12 2024 10:07:07:243 27848 0:149.45 1:149.45 A:3149621954;C:2617992293;G:2634267865;T:3139910090;N:161309 149 149     3149621954 2617992293 2634267865 3139910090 161309 ERX13488954 ERS21188944 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19151 19151 ERR14086547 ERX13488921 ERS21188911 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F2 T2 ZF Con 2h F2 T2 SAMEA116144970 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 2h F2 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:207 27781 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F2_T2.pair1.truncated ZF_Con_2h_F2_T2.pair2.truncated fastq fastq 13863272461.0 46344391.0 ena RUN TAB 19 12 2024 10:07:07:208 27782 0:149.57 1:149.57 A:3792400588;C:3136237717;G:3165201062;T:3769186938;N:246156 149 149     3792400588 3136237717 3165201062 3769186938 246156 ERX13488921 ERS21188911 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19152 19152 ERR14086550 ERX13488924 ERS21188914 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F5 T2 ZF Con 2h F5 T2 SAMEA116144973 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 2h F5 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:210 27787 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F5_T2.pair1.truncated ZF_Con_2h_F5_T2.pair2.truncated fastq fastq 12875582522.0 43072753.0 ena RUN TAB 19 12 2024 10:07:07:211 27788 0:149.46 1:149.46 A:3497197102;C:2940877881;G:2959759457;T:3477623582;N:124500 149 149     3497197102 2940877881 2959759457 3477623582 124500 ERX13488924 ERS21188914 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19153 19153 ERR14086586 ERX13488960 ERS21188950 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F7 T2 ZF Inf 72h F7 T2 SAMEA116145009 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 Inf 72h F7 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F7 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:248 27859 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F7_T2.pair1.truncated ZF_Inf_72h_F7_T2.pair2.truncated fastq fastq 13295980347.0 44467065.0 ena RUN TAB 19 12 2024 10:07:07:249 27860 0:149.50 1:149.50 A:3621424205;C:3027543860;G:3042454743;T:3604321654;N:235885 149 149     3621424205 3027543860 3042454743 3604321654 235885 ERX13488960 ERS21188950 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19154 19154 ERR14086561 ERX13488935 ERS21188925 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F4 T1 ZF Con 72h F4 T1 SAMEA116144984 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 F4 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F4 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:224 27809 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F4_T1.pair1.truncated ZF_Con_72h_F4_T1.pair2.truncated fastq fastq 9938081497.0 33212946.0 ena RUN TAB 19 12 2024 10:07:07:224 27810 0:149.61 1:149.61 A:2721489962;C:2248630062;G:2262566481;T:2705255710;N:139282 149 149     2721489962 2248630062 2262566481 2705255710 139282 ERX13488935 ERS21188925 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19155 19155 ERR14086579 ERX13488953 ERS21188943 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F5 T1 ZF Inf 48h F5 T1 SAMEA116145002 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 Inf 48h F5 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:241 27845 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F5_T1.pair1.truncated ZF_Inf_48h_F5_T1.pair2.truncated fastq fastq 12222927812.0 40990200.0 ena RUN TAB 19 12 2024 10:07:07:242 27846 0:149.10 1:149.10 A:3396661594;C:2718183404;G:2739192225;T:3368673043;N:217546 149 149     3396661594 2718183404 2739192225 3368673043 217546 ERX13488953 ERS21188943 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19156 19156 ERR14086573 ERX13488947 ERS21188937 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F5 T1 ZF Inf 2h F5 T1 SAMEA116144996 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 Inf 2h F5 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:236 27833 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F5_T1.pair1.truncated ZF_Inf_2h_F5_T1.pair2.truncated fastq fastq 10449733742.0 35250991.0 ena RUN TAB 19 12 2024 10:07:07:236 27834 0:148.22 1:148.22 A:2804774831;C:2419904968;G:2439597584;T:2785285420;N:170939 148 148     2804774831 2419904968 2439597584 2785285420 170939 ERX13488947 ERS21188937 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19157 19157 ERR14086568 ERX13488942 ERS21188932 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F5 T2 ZF Inf 24h F5 T2 SAMEA116144991 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 Inf 24h F5 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:231 27823 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F5_T2.pair1.truncated ZF_Inf_24h_F5_T2.pair2.truncated fastq fastq 12646844136.0 42337796.0 ena RUN TAB 19 12 2024 10:07:07:231 27824 0:149.36 1:149.36 A:3482695386;C:2837435668;G:2870976079;T:3455511927;N:225076 149 149     3482695386 2837435668 2870976079 3455511927 225076 ERX13488942 ERS21188932 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19158 19158 ERR14086544 ERX13488918 ERS21188908 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F5 T2 ZF Con 24h F5 T2 SAMEA116144967 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 24h F5 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:204 27775 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F5_T2.pair1.truncated ZF_Con_24h_F5_T2.pair2.truncated fastq fastq 14844040377.0 49765280.0 ena RUN TAB 19 12 2024 10:07:07:204 27776 0:149.14 1:149.14 A:4064105817;C:3361019988;G:3386488696;T:4032154980;N:270896 149 149     4064105817 3361019988 3386488696 4032154980 270896 ERX13488918 ERS21188908 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19159 19159 ERR14086571 ERX13488945 ERS21188935 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F4 T1 ZF Inf 2h F4 T1 SAMEA116144994 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 Inf 2h F4 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F4 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:234 27829 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F4_T1.pair1.truncated ZF_Inf_2h_F4_T1.pair2.truncated fastq fastq 12838150223.0 42953821.0 ena RUN TAB 19 12 2024 10:07:07:234 27830 0:149.44 1:149.44 A:3519614186;C:2900824893;G:2922740944;T:3494741243;N:228957 149 149     3519614186 2900824893 2922740944 3494741243 228957 ERX13488945 ERS21188935 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19160 19160 ERR14086549 ERX13488923 ERS21188913 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F5 T1 ZF Con 2h F5 T1 SAMEA116144972 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 2h F5 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:209 27785 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F5_T1.pair1.truncated ZF_Con_2h_F5_T1.pair2.truncated fastq fastq 11835612468.0 39584841.0 ena RUN TAB 19 12 2024 10:07:07:210 27786 0:149.50 1:149.50 A:3269078282;C:2648809055;G:2674404587;T:3243109727;N:210817 149 149     3269078282 2648809055 2674404587 3243109727 210817 ERX13488923 ERS21188913 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19161 19161 ERR14086542 ERX13488916 ERS21188906 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F4 T2 ZF Con 24h F4 T2 SAMEA116144965 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 24h F4 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F4 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:202 27771 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F4_T2.pair1.truncated ZF_Con_24h_F4_T2.pair2.truncated fastq fastq 13798422139.0 46177289.0 ena RUN TAB 19 12 2024 10:07:07:202 27772 0:149.41 1:149.41 A:3775147943;C:3126239757;G:3146905685;T:3749874746;N:254008 149 149     3775147943 3126239757 3146905685 3749874746 254008 ERX13488916 ERS21188906 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19162 19162 ERR14086552 ERX13488926 ERS21188916 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F2 T2 ZF Con 48h F2 T2 SAMEA116144975 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 48h F2 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:213 27791 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F2_T2.pair1.truncated ZF_Con_48h_F2_T2.pair2.truncated fastq fastq 13264338841.0 44308876.0 ena RUN TAB 19 12 2024 10:07:07:213 27792 0:149.68 1:149.68 A:3659186141;C:2980901976;G:3004156932;T:3619853492;N:240300 149 149     3659186141 2980901976 3004156932 3619853492 240300 ERX13488926 ERS21188916 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19163 19163 ERR14086564 ERX13488938 ERS21188928 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F3 T1 ZF Inf 24h F3 T1 SAMEA116144987 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 Inf 24h F3 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:227 27815 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F3_T1.pair1.truncated ZF_Inf_24h_F3_T1.pair2.truncated fastq fastq 10381791769.0 34725644.0 ena RUN TAB 19 12 2024 10:07:07:227 27816 0:149.48 1:149.48 A:2873405143;C:2324734677;G:2341512339;T:2841957730;N:181880 149 149     2873405143 2324734677 2341512339 2841957730 181880 ERX13488938 ERS21188928 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19164 19164 ERR14086578 ERX13488952 ERS21188942 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F3 T2 ZF Inf 48h F3 T2 SAMEA116145001 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 Inf 48h F3 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:240 27843 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F3_T2.pair1.truncated ZF_Inf_48h_F3_T2.pair2.truncated fastq fastq 11607933528.0 38797282.0 ena RUN TAB 19 12 2024 10:07:07:241 27844 0:149.60 1:149.60 A:3157510185;C:2647554101;G:2661033132;T:3141630885;N:205225 149 149     3157510185 2647554101 2661033132 3141630885 205225 ERX13488952 ERS21188942 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19165 19165 ERR14086585 ERX13488959 ERS21188949 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F6 T2 ZF Inf 72h F6 T2 SAMEA116145008 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 Inf 72h F6 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F6 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:247 27857 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F6_T2.pair1.truncated ZF_Inf_72h_F6_T2.pair2.truncated fastq fastq 14586616716.0 48786392.0 ena RUN TAB 19 12 2024 10:07:07:248 27858 0:149.49 1:149.49 A:4004810052;C:3292146107;G:3307969966;T:3981432519;N:258072 149 149     4004810052 3292146107 3307969966 3981432519 258072 ERX13488959 ERS21188949 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19166 19166 ERR14086569 ERX13488943 ERS21188933 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F3 T1 ZF Inf 2h F3 T1 SAMEA116144992 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 Inf 2h F3 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:232 27825 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F3_T1.pair1.truncated ZF_Inf_2h_F3_T1.pair2.truncated fastq fastq 11019441647.0 36982136.0 ena RUN TAB 19 12 2024 10:07:07:232 27826 0:148.98 1:148.98 A:3037955689;C:2470815294;G:2485099673;T:3025375051;N:195940 148 148     3037955689 2470815294 2485099673 3025375051 195940 ERX13488943 ERS21188933 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19167 19167 ERR14086565 ERX13488939 ERS21188929 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F3 T2 ZF Inf 24h F3 T2 SAMEA116144988 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 Inf 24h F3 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:228 27817 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F3_T2.pair1.truncated ZF_Inf_24h_F3_T2.pair2.truncated fastq fastq 9871958838.0 32967513.0 ena RUN TAB 19 12 2024 10:07:07:229 27818 0:149.72 1:149.72 A:2712574707;C:2241323417;G:2237990565;T:2680027600;N:42549 149 149     2712574707 2241323417 2237990565 2680027600 42549 ERX13488939 ERS21188929 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19168 19168 ERR14086556 ERX13488930 ERS21188920 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F5 T2 ZF Con 48h F5 T2 SAMEA116144979 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 48h F5 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:217 27799 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F5_T2.pair1.truncated ZF_Con_48h_F5_T2.pair2.truncated fastq fastq 11861470651.0 39639855.0 ena RUN TAB 19 12 2024 10:07:07:218 27800 0:149.62 1:149.62 A:3258887757;C:2673190405;G:2689128055;T:3240053301;N:211133 149 149     3258887757 2673190405 2689128055 3240053301 211133 ERX13488930 ERS21188920 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19169 19169 ERR14086543 ERX13488917 ERS21188907 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F5 T1 ZF Con 24h F5 T1 SAMEA116144966 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 24h F5 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:203 27773 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F5_T1.pair1.truncated ZF_Con_24h_F5_T1.pair2.truncated fastq fastq 13831914606.0 46241530.0 ena RUN TAB 19 12 2024 10:07:07:203 27774 0:149.56 1:149.56 A:3799248185;C:3123745954;G:3140306544;T:3768364222;N:249701 149 149     3799248185 3123745954 3140306544 3768364222 249701 ERX13488917 ERS21188907 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19170 19170 ERR14086554 ERX13488928 ERS21188918 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F3 T2 ZF Con 48h F3 T2 SAMEA116144977 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 48h F3 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F3 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:215 27795 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F3_T2.pair1.truncated ZF_Con_48h_F3_T2.pair2.truncated fastq fastq 12448461131.0 41602782.0 ena RUN TAB 19 12 2024 10:07:07:215 27796 0:149.61 1:149.61 A:3389327765;C:2836108569;G:2854509891;T:3368293555;N:221351 149 149     3389327765 2836108569 2854509891 3368293555 221351 ERX13488928 ERS21188918 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19171 19171 ERR14086551 ERX13488925 ERS21188915 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F1 T1 ZF Con 48h F1 T1 SAMEA116144974 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 48h F1 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:211 27789 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F1_T1.pair1.truncated ZF_Con_48h_F1_T1.pair2.truncated fastq fastq 12344084376.0 54459157.0 ena RUN TAB 19 12 2024 10:07:07:212 27790 0:113.33 1:113.33 A:3422797649;C:2748327064;G:2785936911;T:3386774171;N:248581 113 113     3422797649 2748327064 2785936911 3386774171 248581 ERX13488925 ERS21188915 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19172 19172 ERR14086539 ERX13488913 ERS21188903 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F1 T1 ZF Con 24h F1 T1 SAMEA116144962 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 24h F1 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:197 27765 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F1_T1.pair1.truncated ZF_Con_24h_F1_T1.pair2.truncated fastq fastq 10290290855.0 34422082.0 ena RUN TAB 19 12 2024 10:07:07:198 27766 0:149.47 1:149.47 A:2828748546;C:2322992474;G:2336279187;T:2802084735;N:185913 149 149     2828748546 2322992474 2336279187 2802084735 185913 ERX13488913 ERS21188903 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19173 19173 ERR14086563 ERX13488937 ERS21188927 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F2 T2 ZF Inf 24h F2 T2 SAMEA116144986 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 Inf 24h F2 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F2 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:226 27813 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F2_T2.pair1.truncated ZF_Inf_24h_F2_T2.pair2.truncated fastq fastq 13536477558.0 45257672.0 ena RUN TAB 19 12 2024 10:07:07:226 27814 0:149.55 1:149.55 A:3725663504;C:3050152384;G:3076823290;T:3683598880;N:239500 149 149     3725663504 3050152384 3076823290 3683598880 239500 ERX13488937 ERS21188927 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19174 19174 ERR14086545 ERX13488919 ERS21188909 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F1 T2 ZF Con 2h F1 T2 SAMEA116144968 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 2h F1 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F1 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:205 27777 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F1_T2.pair1.truncated ZF_Con_2h_F1_T2.pair2.truncated fastq fastq 11201747073.0 37461080.0 ena RUN TAB 19 12 2024 10:07:07:206 27778 0:149.51 1:149.51 A:3081962381;C:2520875203;G:2541328205;T:3057571709;N:9575 149 149     3081962381 2520875203 2541328205 3057571709 9575 ERX13488919 ERS21188909 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19175 19175 ERR14086577 ERX13488951 ERS21188941 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F3 T1 ZF Inf 48h F3 T1 SAMEA116145000 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 Inf 48h F3 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27841 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F3_T1.pair1.truncated ZF_Inf_48h_F3_T1.pair2.truncated fastq fastq 11531780443.0 49868909.0 ena RUN TAB 19 12 2024 10:07:07:240 27842 0:115.62 1:115.62 A:3218054358;C:2544627851;G:2576550932;T:3192371527;N:175775 115 115     3218054358 2544627851 2576550932 3192371527 175775 ERX13488951 ERS21188941 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19176 19176 ERR14086566 ERX13488940 ERS21188930 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F4 T1 ZF Inf 24h F4 T1 SAMEA116144989 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 Inf 24h F4 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F4 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:229 27819 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F4_T1.pair1.truncated ZF_Inf_24h_F4_T1.pair2.truncated fastq fastq 11576629501.0 38725250.0 ena RUN TAB 19 12 2024 10:07:07:230 27820 0:149.47 1:149.47 A:3206545757;C:2592097810;G:2606700733;T:3171079624;N:205577 149 149     3206545757 2592097810 2606700733 3171079624 205577 ERX13488940 ERS21188930 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19177 19177 ERR14086582 ERX13488956 ERS21188946 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F5 T1 ZF Inf 72h F5 T1 SAMEA116145005 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 Inf 72h F5 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:244 27851 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F5_T1.pair1.truncated ZF_Inf_72h_F5_T1.pair2.truncated fastq fastq 12397801507.0 41450013.0 ena RUN TAB 19 12 2024 10:07:07:245 27852 0:149.55 1:149.55 A:3389701418;C:2810670716;G:2824520271;T:3372689235;N:219867 149 149     3389701418 2810670716 2824520271 3372689235 219867 ERX13488956 ERS21188946 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19178 19178 ERR14086562 ERX13488936 ERS21188926 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F7 T2 ZF Con 72h F7 T2 SAMEA116144985 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 F7 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F7 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:225 27811 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F7_T2.pair1.truncated ZF_Con_72h_F7_T2.pair2.truncated fastq fastq 11568689281.0 38694416.0 ena RUN TAB 19 12 2024 10:07:07:225 27812 0:149.49 1:149.49 A:3162387247;C:2620210879;G:2638016970;T:3147868485;N:205700 149 149     3162387247 2620210879 2638016970 3147868485 205700 ERX13488936 ERS21188926 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19179 19179 ERR14086567 ERX13488941 ERS21188931 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F5 T1 ZF Inf 24h F5 T1 SAMEA116144990 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 Inf 24h F5 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:230 27821 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F5_T1.pair1.truncated ZF_Inf_24h_F5_T1.pair2.truncated fastq fastq 10664451175.0 35656640.0 ena RUN TAB 19 12 2024 10:07:07:231 27822 0:149.54 1:149.54 A:2979287360;C:2367113995;G:2380139534;T:2937759666;N:150620 149 149     2979287360 2367113995 2380139534 2937759666 150620 ERX13488941 ERS21188931 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19180 19180 ERR14086574 ERX13488948 ERS21188938 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F5 T2 ZF Inf 2h F5 T2 SAMEA116144997 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 Inf 2h F5 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:237 27835 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F5_T2.pair1.truncated ZF_Inf_2h_F5_T2.pair2.truncated fastq fastq 13456220858.0 45130746.0 ena RUN TAB 19 12 2024 10:07:07:237 27836 0:149.08 1:149.08 A:3757991654;C:2980420740;G:3002285127;T:3715336913;N:186424 149 149     3757991654 2980420740 3002285127 3715336913 186424 ERX13488948 ERS21188938 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19181 19181 ERR14086570 ERX13488944 ERS21188934 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F3 T2 ZF Inf 2h F3 T2 SAMEA116144993 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 Inf 2h F3 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:233 27827 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F3_T2.pair1.truncated ZF_Inf_2h_F3_T2.pair2.truncated fastq fastq 11155932742.0 37312716.0 ena RUN TAB 19 12 2024 10:07:07:233 27828 0:149.49 1:149.49 A:3110035774;C:2469247298;G:2493445096;T:3083048988;N:155586 149 149     3110035774 2469247298 2493445096 3083048988 155586 ERX13488944 ERS21188934 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19182 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   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                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:222 27807 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   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     3612242281 2968585225 2988176368 3589814432 181369 ERX13488934 ERS21188924 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19183 19183 ERR14086584 ERX13488958 ERS21188948 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F6 T1 ZF Inf 72h F6 T1 SAMEA116145007 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 Inf 72h F6 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F6 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:246 27855 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F6_T1.pair1.truncated ZF_Inf_72h_F6_T1.pair2.truncated fastq fastq 11923216836.0 39846317.0 ena RUN TAB 19 12 2024 10:07:07:247 27856 0:149.62 1:149.62 A:3285592694;C:2678630366;G:2695236989;T:3263545610;N:211177 149 149     3285592694 2678630366 2695236989 3263545610 211177 ERX13488958 ERS21188948 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19184 19184 ERR14086575 ERX13488949 ERS21188939 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F1 T2 ZF Inf 48h F1 T2 SAMEA116144998 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 Inf 48h F1 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F1 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:238 27837 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F1_T2.pair1.truncated ZF_Inf_48h_F1_T2.pair2.truncated fastq fastq 11019995708.0 36865197.0 ena RUN TAB 19 12 2024 10:07:07:238 27838 0:149.46 1:149.46 A:3082432761;C:2435008871;G:2450821136;T:3051565998;N:166942 149 149     3082432761 2435008871 2450821136 3051565998 166942 ERX13488949 ERS21188939 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19185 19185 ERR14086558 ERX13488932 ERS21188922 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F2 T1 ZF Con 72h F2 T1 SAMEA116144981 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 F2 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:220 27803 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F2_T1.pair1.truncated ZF_Con_72h_F2_T1.pair2.truncated fastq fastq 12158516718.0 40627398.0 ena RUN TAB 19 12 2024 10:07:07:221 27804 0:149.63 1:149.63 A:3326615137;C:2756469221;G:2772700363;T:3302562617;N:169380 149 149     3326615137 2756469221 2772700363 3302562617 169380 ERX13488932 ERS21188922 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19186 19186 ERR14086541 ERX13488915 ERS21188905 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F2 T1 ZF Con 24h F2 T1 SAMEA116144964 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 24h F2 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:201 27769 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F2_T1.pair1.truncated ZF_Con_24h_F2_T1.pair2.truncated fastq fastq 11404609454.0 38159925.0 ena RUN TAB 19 12 2024 10:07:07:201 27770 0:149.43 1:149.43 A:3146353279;C:2555600785;G:2577318019;T:3125135234;N:202137 149 149     3146353279 2555600785 2577318019 3125135234 202137 ERX13488915 ERS21188905 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19187 19187 ERR14086572 ERX13488946 ERS21188936 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F4 T2 ZF Inf 2h F4 T2 SAMEA116144995 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 Inf 2h F4 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F4 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:235 27831 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F4_T2.pair1.truncated ZF_Inf_2h_F4_T2.pair2.truncated fastq fastq 11812386851.0 39497047.0 ena RUN TAB 19 12 2024 10:07:07:235 27832 0:149.54 1:149.54 A:3313507246;C:2601867632;G:2622018552;T:3274784725;N:208696 149 149     3313507246 2601867632 2622018552 3274784725 208696 ERX13488946 ERS21188936 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19188 19188 ERR14086553 ERX13488927 ERS21188917 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F3 T1 ZF Con 48h F3 T1 SAMEA116144976 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 48h F3 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F3 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:214 27793 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F3_T1.pair1.truncated ZF_Con_48h_F3_T1.pair2.truncated fastq fastq 12860940085.0 43001318.0 ena RUN TAB 19 12 2024 10:07:07:214 27794 0:149.54 1:149.54 A:3516221949;C:2916982714;G:2940303713;T:3487420693;N:11016 149 149     3516221949 2916982714 2940303713 3487420693 11016 ERX13488927 ERS21188917 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19189 19189 ERR14086557 ERX13488931 ERS21188921 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F1 T1 ZF Con 72h F1 T1 SAMEA116144980 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 F1 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:219 27801 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F1_T1.pair1.truncated ZF_Con_72h_F1_T1.pair2.truncated fastq fastq 12099743905.0 40432008.0 ena RUN TAB 19 12 2024 10:07:07:219 27802 0:149.63 1:149.63 A:3308799221;C:2749018579;G:2763091293;T:3278620227;N:214585 149 149     3308799221 2749018579 2763091293 3278620227 214585 ERX13488931 ERS21188921 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19190 19190 ERR14086583 ERX13488957 ERS21188947 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 r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F5 T2 ZF Inf 72h F5 T2 SAMEA116145006 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 Inf 72h F5 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:245 27853 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F5_T2.pair1.truncated ZF_Inf_72h_F5_T2.pair2.truncated fastq fastq 14068176128.0 47037267.0 ena RUN TAB 19 12 2024 10:07:07:246 27854 0:149.54 1:149.54 A:3862187166;C:3174538324;G:3190936465;T:3840265949;N:248224 149 149     3862187166 3174538324 3190936465 3840265949 248224 ERX13488957 ERS21188947 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
52165 52165 SRR18181441 SRX14328405 SRS12144036 SRP194254 PRJNA540466 Characterization of the zebrafish cell landscape at single cell resolution GSE130487 Transcriptome Analysis Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.   pubmed:34660600   Gill6 GSM5924279   source name:gill|strain:Tubingen|tissue:gill|genotype:wild type Gill6 Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes. gill   Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol   strain:Tubingen|tissue:gill|genotype:wild type GSM5924279 GSM5924279: Gill6; Danio rerio; RNA Seq GSM5924279   1 Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol GEO Accession:GSM5924279 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP194254   assembly:Danio rerio GRCz10|intentional duplicate Gill6.bam bam 19809945600.0 66033152.0 GSM5924279 r1 0:150 1:150 A:5239766235;C:3329504882;G:3343228185;T:7895078269;N:2368029 150 150     5239766235 3329504882 3343228185 7895078269 2368029 SRX14328405 SRS12144036 SRA880843 GEO Zhejiang University 2 0.0 0.70563 0.0 0.05162 1.0 0.8565   0.67358 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate microwellseq   China 2022-03-01 Undetermined Multi-stage Gill Respiratory System
52166 52166 SRR18181440 SRX14328404 SRS12144035 SRP194254 PRJNA540466 Characterization of the zebrafish cell landscape at single cell resolution GSE130487 Transcriptome Analysis Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.   pubmed:34660600   Gill5 GSM5924278   source name:gill|strain:Tubingen|tissue:gill|genotype:wild type Gill5 Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes. gill   Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol   strain:Tubingen|tissue:gill|genotype:wild type GSM5924278 GSM5924278: Gill5; Danio rerio; RNA Seq GSM5924278   1 Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol GEO Accession:GSM5924278 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP194254   assembly:Danio rerio GRCz10|intentional duplicate Gill5.bam bam 21230554200.0 70768514.0 GSM5924278 r1 0:150 1:150 A:5525026007;C:3634039752;G:3645652541;T:8423300924;N:2534976 150 150     5525026007 3634039752 3645652541 8423300924 2534976 SRX14328404 SRS12144035 SRA880843 GEO Zhejiang University 2 2e-05 0.7412 0.0 0.05354 0.99997 0.85462 0.0 0.66686 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate microwellseq   China 2022-03-01 Undetermined Multi-stage Gill Respiratory System
52167 52167 SRR18181439 SRX14328403 SRS12144034 SRP194254 PRJNA540466 Characterization of the zebrafish cell landscape at single cell resolution GSE130487 Transcriptome Analysis Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.   pubmed:34660600   Gill3 GSM5924277   source name:gill|strain:Tubingen|tissue:gill|genotype:wild type Gill3 Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes. gill   Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol   strain:Tubingen|tissue:gill|genotype:wild type GSM5924277 GSM5924277: Gill3; Danio rerio; RNA Seq GSM5924277   1 Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol GEO Accession:GSM5924277 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP194254   assembly:Danio rerio GRCz10|intentional duplicate Gill3.bam bam 21579822900.0 71932743.0 GSM5924277 r1 0:150 1:150 A:5441997035;C:3521528250;G:3625669551;T:8988770258;N:1857806 150 150     5441997035 3521528250 3625669551 8988770258 1857806 SRX14328403 SRS12144034 SRA880843 GEO Zhejiang University 2 0.0 0.74255 0.0 0.03463 1.0 0.81434   0.586 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate microwellseq   China 2022-03-01 Undetermined Multi-stage Gill Respiratory System
67836 67836 SRR17386276 SRX13560365 SRS11453104 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G7 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S131 S131 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_7dpi3_Clean_Data1.fq.gz Gill_7dpi3_Clean_Data2.fq.gz fastq fastq 6714068679.0 23990941.0 Gill 7dpi3 Clean Data1.fq.gz 0:139.94 1:139.92 A:1763959035;C:1585978862;G:1593569642;T:1770413859;N:147281 139 139     1763959035 1585978862 1593569642 1770413859 147281 SRX13560365 SRS11453104 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.9346 0.93604 0.05602 0.05525 0.69877 0.69761 0.5006 0.50091 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67837 67837 SRR17386277 SRX13560364 SRS11453103 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G7 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 8|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S130 S130 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_7dpi2_Clean_Data1.fq.gz Gill_7dpi2_Clean_Data2.fq.gz fastq fastq 6651799504.0 23755238.0 Gill 7dpi2 Clean Data1.fq.gz 0:140.01 1:140.00 A:1739818732;C:1574969869;G:1589121073;T:1747742026;N:147804 140 140     1739818732 1574969869 1589121073 1747742026 147804 SRX13560364 SRS11453103 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.93216 0.93204 0.05441 0.05411 0.70021 0.70017 0.49971 0.50022 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67838 67838 SRR17386278 SRX13560363 SRS11453102 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G7 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S129 S129 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_7dpi1_Clean_Data1.fq.gz Gill_7dpi1_Clean_Data2.fq.gz fastq fastq 4992822830.0 17852500.0 Gill 7dpi1 Clean Data1.fq.gz 0:139.84 1:139.83 A:1332570758;C:1157260526;G:1174499594;T:1328481612;N:10340 139 139     1332570758 1157260526 1174499594 1328481612 10340 SRX13560363 SRS11453102 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.9281 0.93065 0.06937 0.06833 0.69033 0.68893 0.50068 0.50026 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67839 67839 SRR17386279 SRX13560362 SRS11453101 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G3 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S128 S128 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_3dpi3_Clean_Data1.fq.gz Gill_3dpi3_Clean_Data2.fq.gz fastq fastq 6997831816.0 24954040.0 Gill 3dpi3 Clean Data1.fq.gz 0:140.22 1:140.21 A:1830864881;C:1655547632;G:1672630082;T:1838637853;N:151368 140 140     1830864881 1655547632 1672630082 1838637853 151368 SRX13560362 SRS11453101 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.93226 0.93407 0.04804 0.04727 0.71981 0.71881 0.48198 0.48333 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67840 67840 SRR17386280 SRX13560361 SRS11453100 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G3 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S127 S127 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_3dpi2_Clean_Data1.fq.gz Gill_3dpi2_Clean_Data2.fq.gz fastq fastq 7042078942.0 25114470.0 Gill 3dpi2 Clean Data1.fq.gz 0:140.21 1:140.19 A:1839895370;C:1667692247;G:1684937624;T:1849401074;N:152627 140 140     1839895370 1667692247 1684937624 1849401074 152627 SRX13560361 SRS11453100 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.93037 0.93106 0.04787 0.04704 0.71956 0.71833 0.4789 0.48397 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67841 67841 SRR17386281 SRX13560360 SRS11453099 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G3 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S126 S126 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_3dpi1_Clean_Data1.fq.gz Gill_3dpi1_Clean_Data2.fq.gz fastq fastq 6795179593.0 24546282.0 Gill 3dpi1 Clean Data1.fq.gz 0:138.41 1:138.42 A:1740617128;C:1653484959;G:1667383107;T:1733667548;N:26851 138 138     1740617128 1653484959 1667383107 1733667548 26851 SRX13560360 SRS11453099 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.93975 0.93965 0.04328 0.04269 0.71908 0.72032 0.47917 0.47612 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67842 67842 SRR17386282 SRX13560359 SRS11453098 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         ck 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S125 S125 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_con3_Clean_Data1.fq.gz Gill_con3_Clean_Data2.fq.gz fastq fastq 6532623508.0 23299642.0 Gill con3 Clean Data1.fq.gz 0:140.19 1:140.18 A:1719338437;C:1532877064;G:1551680948;T:1728585867;N:141192 140 140     1719338437 1532877064 1551680948 1728585867 141192 SRX13560359 SRS11453098 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.93634 0.93701 0.0531 0.05253 0.72936 0.72977 0.48876 0.49167 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67843 67843 SRR17386283 SRX13560358 SRS11453097 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         ck 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S124 S124 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_con2_Clean_Data1.fq.gz Gill_con2_Clean_Data2.fq.gz fastq fastq 5961805472.0 21275022.0 Gill con2 Clean Data1.fq.gz 0:140.12 1:140.11 A:1562509100;C:1405898016;G:1423494829;T:1569772023;N:131504 140 140     1562509100 1405898016 1423494829 1569772023 131504 SRX13560358 SRS11453097 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.93445 0.93628 0.04993 0.04957 0.73182 0.73077 0.48248 0.49573 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67844 67844 SRR17386284 SRX13560357 SRS11453096 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         ck 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S123 S123 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_con1_Clean_Data1.fq.gz Gill_con1_Clean_Data2.fq.gz fastq fastq 5140938459.0 18343430.0 Gill con1 Clean Data1.fq.gz 0:140.14 1:140.12 A:1372431897;C:1190016635;G:1209788123;T:1368690050;N:11754 140 140     1372431897 1190016635 1209788123 1368690050 11754 SRX13560357 SRS11453096 SRA1350370 Northwest A&F University|College of Animal Science and Technology Northwest A&F University 2 0.92642 0.93067 0.06487 0.06429 0.72529 0.72403 0.51099 0.51071 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
68950 68950 SRR18254619 SRX14395875 SRS12205981 SRP362863 PRJNA813520 Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia GSE198044 Transcriptome Analysis The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.   pubmed:35710785   Gill tissue combined normoxia and hypoxia GSM5936455   tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:normoxia and hypoxia samples combined Gill tissue combined normoxia and hypoxia Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries. Distal gill filament   Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   genotype:ETvmat2:GFP|treatment:normoxia and hypoxia samples combined GSM5936455 GSM5936455: Gill tissue combined normoxia and hypoxia; Danio rerio; RNA Seq GSM5936455 r1 GSM5936455 1 Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP362863   loader:fastq load.py HN_SC_I1.fastq.gz HN_SC_R1.fastq.gz HN_SC_R2.fastq.gz fastq fastq fastq 20585326398.0 226212378.0 GSM5936455 r1 0:8 1:28 2:55 A:3704476968;C:2664002498;G:2831788454;T:3232756993;N:8655877 8 28 55   3704476968 2664002498 2831788454 3232756993 8655877 SRX14395875 SRS12205981 SRA1392368 Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) 1 0.92742   0.15723   0.83011   0.68192   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Canada 2022-03-07 Undetermined Undetermined Gill Respiratory System
68951 68951 SRR18254620 SRX14395875 SRS12205981 SRP362863 PRJNA813520 Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia GSE198044 Transcriptome Analysis The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.   pubmed:35710785   Gill tissue combined normoxia and hypoxia GSM5936455   tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:normoxia and hypoxia samples combined Gill tissue combined normoxia and hypoxia Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries. Distal gill filament   Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   genotype:ETvmat2:GFP|treatment:normoxia and hypoxia samples combined GSM5936455 GSM5936455: Gill tissue combined normoxia and hypoxia; Danio rerio; RNA Seq GSM5936455 r1 GSM5936455 1 Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP362863   loader:fastq load.py HN_Barcode_I1.fastq.gz HN_Barcode_R1.fastq.gz HN_Barcode_R2.fastq.gz fastq fastq fastq 1029719145.0 11315595.0 GSM5936455 r2 0:8 1:28 2:55 A:465061193;C:46504427;G:62910508;T:47445353;N:436244 8 28 55   465061193 46504427 62910508 47445353 436244 SRX14395875 SRS12205981 SRA1392368 Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) 1 0.56414   0.53829   0.99977   0.11976   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Canada 2022-03-07 Undetermined Undetermined Gill Respiratory System
68952 68952 SRR18254621 SRX14395874 SRS12205982 SRP362863 PRJNA813520 Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia GSE198044 Transcriptome Analysis The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.   pubmed:35710785   Gill tissue 14d hypoxia GSM5936454   tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of hypoxia Gill tissue 14d hypoxia Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries. Distal gill filament   Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   genotype:ETvmat2:GFP|treatment:14 days of hypoxia GSM5936454 GSM5936454: Gill tissue 14d hypoxia; Danio rerio; RNA Seq GSM5936454 r1 GSM5936454 1 Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP362863   loader:fastq load.py N1_SC_I1.fastq.gz N1_SC_R1.fastq.gz N1_SC_R2.fastq.gz fastq fastq fastq 20495108725.0 225220975.0 GSM5936454 r1 0:8 1:28 2:55 A:3710830156;C:2666739789;G:2832783659;T:3168227781;N:8572240 8 28 55   3710830156 2666739789 2832783659 3168227781 8572240 SRX14395874 SRS12205982 SRA1392368 Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) 1 0.92266   0.14929   0.83849   0.61082   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Canada 2022-03-07 Undetermined Undetermined Gill Respiratory System
68953 68953 SRR18254622 SRX14395874 SRS12205982 SRP362863 PRJNA813520 Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia GSE198044 Transcriptome Analysis The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.   pubmed:35710785   Gill tissue 14d hypoxia GSM5936454   tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of hypoxia Gill tissue 14d hypoxia Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries. Distal gill filament   Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   genotype:ETvmat2:GFP|treatment:14 days of hypoxia GSM5936454 GSM5936454: Gill tissue 14d hypoxia; Danio rerio; RNA Seq GSM5936454 r1 GSM5936454 1 Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP362863   loader:fastq load.py N1_Barcode_I1.fastq.gz N1_Barcode_R1.fastq.gz N1_Barcode_R2.fastq.gz fastq fastq fastq 1417514644.0 15577084.0 GSM5936454 r2 0:8 1:28 2:55 A:647753176;C:53490237;G:81081706;T:73804327;N:610174 8 28 55   647753176 53490237 81081706 73804327 610174 SRX14395874 SRS12205982 SRA1392368 Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) 1 0.56618   0.54862   0.99973   0.06569   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Canada 2022-03-07 Undetermined Undetermined Gill Respiratory System
68954 68954 SRR18254623 SRX14395873 SRS12205980 SRP362863 PRJNA813520 Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia GSE198044 Transcriptome Analysis The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.   pubmed:35710785   Gill tissue 14d normoxia GSM5936453   tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of normoxia Gill tissue 14d normoxia Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries. Distal gill filament   Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   genotype:ETvmat2:GFP|treatment:14 days of normoxia GSM5936453 GSM5936453: Gill tissue 14d normoxia; Danio rerio; RNA Seq GSM5936453 r1 GSM5936453 1 Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP362863   loader:fastq load.py H1_SC_I1.fastq.gz H1_SC_R1.fastq.gz H1_SC_R2.fastq.gz fastq fastq fastq 23487401392.0 258103312.0 GSM5936453 r1 0:8 1:28 2:55 A:4264761201;C:2967126758;G:3075434435;T:3878445482;N:9914284 8 28 55   4264761201 2967126758 3075434435 3878445482 9914284 SRX14395873 SRS12205980 SRA1392368 Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) 1 0.9248   0.16768   0.81586   0.61578   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Canada 2022-03-07 Undetermined Undetermined Gill Respiratory System
68955 68955 SRR18254624 SRX14395873 SRS12205980 SRP362863 PRJNA813520 Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia GSE198044 Transcriptome Analysis The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.   pubmed:35710785   Gill tissue 14d normoxia GSM5936453   tissue:Distal gill filament|genotype:ETvmat2:GFP|treatment:14 days of normoxia Gill tissue 14d normoxia Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries. Distal gill filament   Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   genotype:ETvmat2:GFP|treatment:14 days of normoxia GSM5936453 GSM5936453: Gill tissue 14d normoxia; Danio rerio; RNA Seq GSM5936453 r1 GSM5936453 1 Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP362863   loader:fastq load.py H1_Barcode_I1.fastq.gz H1_Barcode_R1.fastq.gz H1_Barcode_R2.fastq.gz fastq fastq fastq 1333671703.0 14655733.0 GSM5936453 r2 0:8 1:28 2:55 A:599872306;C:66845042;G:83153279;T:55613709;N:580979 8 28 55   599872306 66845042 83153279 55613709 580979 SRX14395873 SRS12205980 SRA1392368 Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC) 1 0.55243   0.52271   0.99935   0.18823   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Canada 2022-03-07 Undetermined Undetermined Gill Respiratory System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;