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We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 7 mpf zebrafish replicate3", "SAMD00152437", null, "sample name:g07 3|age:7 month|biological replicate:3|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152437", "DRX153108", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152437", null, null, null, 1104355400.0, 5521777.0, "DRR162489", "0:100 1:100", "A:293305974;C:258987844;G:260252632;T:291752232;N:56718", 100, 100, null, null, 293305974, 258987844, 260252632, 291752232, 56718, "DRX153108", "DRS083169", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.94175, 0.93079, 0.07979, 0.07843, 0.7105, 0.7119, 0.5251, 0.52859, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Gill", "Respiratory System"], [253, "DRR162488", "DRX153107", "DRS083168", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 7 mpf zebrafish replicate2", "SAMD00152436", null, "sample name:g07 2|age:7 month|biological replicate:2|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152436", "DRX153107", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152436", null, null, null, 843955600.0, 4219778.0, "DRR162488", "0:100 1:100", "A:223801058;C:198393089;G:199123839;T:222593773;N:43841", 100, 100, null, null, 223801058, 198393089, 199123839, 222593773, 43841, "DRX153107", "DRS083168", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.94491, 0.93727, 0.08987, 0.08908, 0.7217, 0.72454, 0.53198, 0.53231, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Gill", "Respiratory System"], [254, "DRR162487", "DRX153106", "DRS083167", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 7 mpf zebrafish replicate1", "SAMD00152435", null, "sample name:g07 1|age:7 month|biological replicate:1|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152435", "DRX153106", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152435", null, null, null, 910082000.0, 4550410.0, "DRR162487", "0:100 1:100", "A:241668250;C:213411555;G:214645944;T:240311041;N:45210", 100, 100, null, null, 241668250, 213411555, 214645944, 240311041, 45210, "DRX153106", "DRS083167", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.94282, 0.93321, 0.08487, 0.08288, 0.7077, 0.71045, 0.52995, 0.52638, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Gill", "Respiratory System"], [255, "DRR162486", "DRX153105", "DRS083166", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 2 mpf zebrafish replicate5", "SAMD00152434", null, "sample name:g02 5|age:2 month|biological replicate:5|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152434", "DRX153105", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152434", null, null, null, 1270126600.0, 6350633.0, "DRR162486", "0:100 1:100", "A:342076596;C:293249973;G:295429735;T:339306175;N:64121", 100, 100, null, null, 342076596, 293249973, 295429735, 339306175, 64121, "DRX153105", "DRS083166", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.9321, 0.91652, 0.09414, 0.09195, 0.70084, 0.70412, 0.52077, 0.51571, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Gill", "Respiratory System"], [256, "DRR162485", "DRX153104", "DRS083165", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 2 mpf zebrafish replicate4", "SAMD00152433", null, "sample name:g02 4|age:2 month|biological replicate:4|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152433", "DRX153104", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152433", null, null, null, 835205000.0, 4176025.0, "DRR162485", "0:100 1:100", "A:224993396;C:192858928;G:193779680;T:223531224;N:41772", 100, 100, null, null, 224993396, 192858928, 193779680, 223531224, 41772, "DRX153104", "DRS083165", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.9392, 0.92364, 0.08708, 0.08554, 0.70579, 0.71017, 0.53067, 0.52045, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Gill", "Respiratory System"], [257, "DRR162484", "DRX153103", "DRS083164", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 2 mpf zebrafish replicate3", "SAMD00152432", null, "sample name:g02 3|age:2 month|biological replicate:3|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152432", "DRX153103", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152432", null, null, null, 1038999000.0, 5194995.0, "DRR162484", "0:100 1:100", "A:278673674;C:241111198;G:242737620;T:276422623;N:53885", 100, 100, null, null, 278673674, 241111198, 242737620, 276422623, 53885, "DRX153103", "DRS083164", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.92129, 0.9116, 0.08334, 0.0814, 0.71707, 0.71821, 0.5407, 0.53611, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Gill", "Respiratory System"], [258, "DRR162483", "DRX153102", "DRS083163", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 2 mpf zebrafish replicate2", "SAMD00152431", null, "sample name:g02 2|age:2 month|biological replicate:2|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152431", "DRX153102", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152431", null, null, null, 632886400.0, 3164432.0, "DRR162483", "0:100 1:100", "A:169214113;C:147628963;G:147454557;T:168556741;N:32026", 100, 100, null, null, 169214113, 147628963, 147454557, 168556741, 32026, "DRX153102", "DRS083163", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.93019, 0.91653, 0.08504, 0.08547, 0.69367, 0.70707, 0.50674, 0.50918, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Gill", "Respiratory System"], [259, "DRR162482", "DRX153101", "DRS083162", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "gill sample from 2 mpf zebrafish replicate1", "SAMD00152430", null, "sample name:g02 1|age:2 month|biological replicate:1|tissue:gill", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152430", "DRX153101", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152430", null, null, null, 1323105600.0, 6615528.0, "DRR162482", "0:100 1:100", "A:355611103;C:306237205;G:307478272;T:353712733;N:66287", 100, 100, null, null, 355611103, 306237205, 307478272, 353712733, 66287, "DRX153101", "DRS083162", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.93808, 0.92302, 0.08542, 0.08367, 0.69477, 0.69897, 0.52278, 0.50546, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:221 27805", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_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, null, null, 2965060471, 2438948465, 2454160636, 2948358895, 191480, "ERX13488933", "ERS21188923", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:206 27779", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 4063197170, 3359903309, 3389720319, 4045034265, 144295, "ERX13488920", "ERS21188910", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:243 27849", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3754535055, 3089295285, 3114000296, 3730455705, 191895, "ERX13488955", "ERS21188945", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:199 27767", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 2875878023, 2351334168, 2367670600, 2855687426, 8841, "ERX13488914", "ERS21188904", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:216 27797", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3556627514, 2927267468, 2954512353, 3531914408, 229225, "ERX13488929", "ERS21188919", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:208 27783", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 2712516144, 2185151856, 2203905915, 2694465752, 8273, "ERX13488922", "ERS21188912", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27839", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 2850649951, 2367895411, 2362604415, 2819029152, 89841, "ERX13488950", "ERS21188940", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:242 27847", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3149621954, 2617992293, 2634267865, 3139910090, 161309, "ERX13488954", "ERS21188944", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:207 27781", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3792400588, 3136237717, 3165201062, 3769186938, 246156, "ERX13488921", "ERS21188911", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:210 27787", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3497197102, 2940877881, 2959759457, 3477623582, 124500, "ERX13488924", "ERS21188914", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:248 27859", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3621424205, 3027543860, 3042454743, 3604321654, 235885, "ERX13488960", "ERS21188950", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:224 27809", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_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, null, null, 2721489962, 2248630062, 2262566481, 2705255710, 139282, "ERX13488935", "ERS21188925", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:241 27845", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3396661594, 2718183404, 2739192225, 3368673043, 217546, "ERX13488953", "ERS21188943", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:236 27833", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 2804774831, 2419904968, 2439597584, 2785285420, 170939, "ERX13488947", "ERS21188937", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:231 27823", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3482695386, 2837435668, 2870976079, 3455511927, 225076, "ERX13488942", "ERS21188932", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:204 27775", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 4064105817, 3361019988, 3386488696, 4032154980, 270896, "ERX13488918", "ERS21188908", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:234 27829", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3519614186, 2900824893, 2922740944, 3494741243, 228957, "ERX13488945", "ERS21188935", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:209 27785", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3269078282, 2648809055, 2674404587, 3243109727, 210817, "ERX13488923", "ERS21188913", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:202 27771", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3775147943, 3126239757, 3146905685, 3749874746, 254008, "ERX13488916", "ERS21188906", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:213 27791", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3659186141, 2980901976, 3004156932, 3619853492, 240300, "ERX13488926", "ERS21188916", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:227 27815", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 2873405143, 2324734677, 2341512339, 2841957730, 181880, "ERX13488938", "ERS21188928", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:240 27843", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3157510185, 2647554101, 2661033132, 3141630885, 205225, "ERX13488952", "ERS21188942", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:247 27857", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 4004810052, 3292146107, 3307969966, 3981432519, 258072, "ERX13488959", "ERS21188949", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:232 27825", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3037955689, 2470815294, 2485099673, 3025375051, 195940, "ERX13488943", "ERS21188933", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:228 27817", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 2712574707, 2241323417, 2237990565, 2680027600, 42549, "ERX13488939", "ERS21188929", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:217 27799", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3258887757, 2673190405, 2689128055, 3240053301, 211133, "ERX13488930", "ERS21188920", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:203 27773", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3799248185, 3123745954, 3140306544, 3768364222, 249701, "ERX13488917", "ERS21188907", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:215 27795", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3389327765, 2836108569, 2854509891, 3368293555, 221351, "ERX13488928", "ERS21188918", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:211 27789", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3422797649, 2748327064, 2785936911, 3386774171, 248581, "ERX13488925", "ERS21188915", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:197 27765", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 2828748546, 2322992474, 2336279187, 2802084735, 185913, "ERX13488913", "ERS21188903", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:226 27813", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3725663504, 3050152384, 3076823290, 3683598880, 239500, "ERX13488937", "ERS21188927", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:205 27777", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3081962381, 2520875203, 2541328205, 3057571709, 9575, "ERX13488919", "ERS21188909", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27841", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3218054358, 2544627851, 2576550932, 3192371527, 175775, "ERX13488951", "ERS21188941", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:229 27819", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3206545757, 2592097810, 2606700733, 3171079624, 205577, "ERX13488940", "ERS21188930", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:244 27851", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3389701418, 2810670716, 2824520271, 3372689235, 219867, "ERX13488956", "ERS21188946", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:225 27811", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_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, null, null, 3162387247, 2620210879, 2638016970, 3147868485, 205700, "ERX13488936", "ERS21188926", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:230 27821", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 2979287360, 2367113995, 2380139534, 2937759666, 150620, "ERX13488941", "ERS21188931", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:237 27835", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3757991654, 2980420740, 3002285127, 3715336913, 186424, "ERX13488948", "ERS21188938", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:233 27827", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3110035774, 2469247298, 2493445096, 3083048988, 155586, "ERX13488944", "ERS21188934", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [19182, "ERR14086560", "ERX13488934", "ERS21188924", "ERP165174", "PRJEB81327", "A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis", "420c6801-49a8-433c-9e91-52e1fc6cc95a", "Other", "Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h F3 T2", "ZF Con 72h F3 T2", "SAMEA116144983", "CEH,Center for Evolutionary Hologenomics", "ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F3 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F3 T2|scientific name:Danio rerio|status:control|tissue type:gill", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:222 27807", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_F3_T2.pair1.truncated ZF_Con_72h_F3_T2.pair2.truncated", "fastq fastq", 13158999675.0, 43988093.0, "ena RUN TAB 19 12 2024 10:07:07:223 27808", "0:149.57 1:149.57", "A:3612242281;C:2968585225;G:2988176368;T:3589814432;N:181369", 149, 149, null, null, 3612242281, 2968585225, 2988176368, 3589814432, 181369, "ERX13488934", "ERS21188924", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:246 27855", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3285592694, 2678630366, 2695236989, 3263545610, 211177, "ERX13488958", "ERS21188948", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:238 27837", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3082432761, 2435008871, 2450821136, 3051565998, 166942, "ERX13488949", "ERS21188939", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:220 27803", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_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, null, null, 3326615137, 2756469221, 2772700363, 3302562617, 169380, "ERX13488932", "ERS21188922", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:201 27769", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3146353279, 2555600785, 2577318019, 3125135234, 202137, "ERX13488915", "ERS21188905", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:235 27831", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3313507246, 2601867632, 2622018552, 3274784725, 208696, "ERX13488946", "ERS21188936", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:214 27793", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_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, null, null, 3516221949, 2916982714, 2940303713, 3487420693, 11016, "ERX13488927", "ERS21188917", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF Con 72h 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:219 27801", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_Con_72h_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, null, null, 3308799221, 2749018579, 2763091293, 3278620227, 214585, "ERX13488931", "ERS21188921", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [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 responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.", "ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01", null, "ZF 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", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 19 12 2024 10:07:07:245 27853", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP165174", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19", "ZF_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, null, null, 3862187166, 3174538324, 3190936465, 3840265949, 248224, "ERX13488957", "ERS21188947", "ERA31046805", "ceh,center for evolutionary hologenomics|European Nucleotide Archive", "ceh,center for evolutionary hologenomics", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-11-01", "Undetermined", "Undetermined", "Gill", "Respiratory System"], [38065, "SRR1524239", "SRX661004", "SRS665979", "SRP044781", "PRJNA255848", "Danio rerio Transcriptome", "PRJNA255848", "Transcriptome Analysis", "Transcriptome analysis of 12 zebrafish tissues", "parent bioproject:PRJNA255979", "pubmed:27189481", "Zebrafish gills", "Zebrafish gills", "F Dr 3", null, "strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Gills|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish gills", "F Dr 3", "F Dr 3", "Total RNA was qualified using an Agilent BioAnalyzer and 1 \u00b5g was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP044781", null, null, "F_Dr_3_CTTGTA_L002_R1.fastq.gz F_Dr_3_CTTGTA_L002_R2.fastq.gz", "fastq fastq", 10894423200.0, 54472116.0, "F Dr 3 files", "0:100 1:100", "A:2975649534;C:2475294028;G:2539728405;T:2894423141;N:9328092", 100, 100, null, null, 2975649534, 2475294028, 2539728405, 2894423141, 9328092, "SRX661004", "SRS665979", "SRA176464", "INRA|Fish Physiology and Genomics", "INRA PhyloFish", 2, 0.9252, 0.9044, 0.11199, 0.10966, 0.69138, 0.69471, 0.50738, 0.50515, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "France", "2015-07-24", "Adult", "Adult", "Gill", "Respiratory System"], [38275, "SRR1609740", "SRX730393", "SRS719614", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "gill10", "GSM1523035", null, "source name:gill|tissue:gill|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "gill10", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "gill", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:gill|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523035", "GSM1523035: gill10; Danio rerio; RNA Seq", "GSM1523035", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523035", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "gill10_2.fq.gz gill10_1.fq.gz", "fastq fastq", 3808228200.0, 19041141.0, "GSM1523035 r1", "0:100 1:100", "A:1024211062;C:886771339;G:878140821;T:1019042838;N:62140", 100, 100, null, null, 1024211062, 886771339, 878140821, 1019042838, 62140, "SRX730393", "SRS719614", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.9378, 0.93058, 0.07663, 0.07682, 0.73632, 0.73894, 0.50829, 0.50911, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Gill", "Respiratory System"], [38276, "SRR1609739", "SRX730392", "SRS719613", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "gill18", "GSM1523034", null, "source name:gill|tissue:gill|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "gill18", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "gill", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:gill|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523034", "GSM1523034: gill18; Danio rerio; RNA Seq", "GSM1523034", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523034", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "gill18_2.fq.gz gill18_1.fq.gz", "fastq fastq", 3364143200.0, 16820716.0, "GSM1523034 r1", "0:100 1:100", "A:910167069;C:776115825;G:769784486;T:908021630;N:54190", 100, 100, null, null, 910167069, 776115825, 769784486, 908021630, 54190, "SRX730392", "SRS719613", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.93522, 0.92726, 0.09078, 0.09182, 0.69649, 0.70041, 0.49571, 0.5016, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Gill", "Respiratory System"], [38277, "SRR1609738", "SRX730391", "SRS719612", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "gill28", "GSM1523033", null, "source name:gill|tissue:gill|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "gill28", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "gill", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:gill|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523033", "GSM1523033: gill28; Danio rerio; RNA Seq", "GSM1523033", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523033", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "gill28_1.fq.gz gill28_2.fq.gz", "fastq fastq", 3195350200.0, 15976751.0, "GSM1523033 r1", "0:100 1:100", "A:863344322;C:737593661;G:734637604;T:859709733;N:64880", 100, 100, null, null, 863344322, 737593661, 734637604, 859709733, 64880, "SRX730391", "SRS719612", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.93495, 0.93105, 0.07061, 0.07137, 0.70792, 0.70999, 0.51509, 0.52042, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Gill", "Respiratory System"], [39705, "SRR3579899", "SRX1796667", "SRS1464820", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 12h gill 3", "GSM2176256", null, "source name:gill|tissue:gill|species:zebrafish|replicate:3|time point:12h|temperature:8 degreeC|age:6 mpf", "zebrafish 8 12h gill 3", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "tissue:gill|species:zebrafish|replicate:3|time point:12h|temperature:8 degreeC|age:6 mpf", "GSM2176256", "GSM2176256: zebrafish 8 12h gill 3; Danio rerio; RNA Seq", "GSM2176256", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2176256", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "AZ5.R2.fastq.gz AZ5.R1.fastq.gz", "fastq fastq", 3660879450.0, 16793025.0, "GSM2176256 r1", "0:109 1:109", "A:976201248;C:849396723;G:852689371;T:979773691;N:2818417", 109, 109, null, null, 976201248, 849396723, 852689371, 979773691, 2818417, "SRX1796667", "SRS1464820", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.93826, 0.94162, 0.09632, 0.09581, 0.69292, 0.69386, 0.46649, 0.46447, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-05-24", "Adult", "Adult", "Gill", "Respiratory System"], [39706, "SRR3579898", "SRX1796666", "SRS1464819", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 6h gill 3", "GSM2176255", null, "source name:gill|tissue:gill|species:zebrafish|replicate:3|time point:6h|temperature:8 degreeC|age:6 mpf", "zebrafish 8 6h gill 3", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "tissue:gill|species:zebrafish|replicate:3|time point:6h|temperature:8 degreeC|age:6 mpf", "GSM2176255", "GSM2176255: zebrafish 8 6h gill 3; Danio rerio; RNA Seq", "GSM2176255", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2176255", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "AZ4.R2.fastq.gz AZ4.R1.fastq.gz", "fastq fastq", 3296611478.0, 15122071.0, "GSM2176255 r1", "0:109 1:109", "A:878524477;C:766752274;G:767841114;T:880950979;N:2542634", 109, 109, null, null, 878524477, 766752274, 767841114, 880950979, 2542634, "SRX1796666", "SRS1464819", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.94142, 0.94349, 0.08715, 0.08682, 0.69073, 0.69266, 0.50384, 0.49966, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-05-24", "Adult", "Adult", "Gill", "Respiratory System"], [39707, "SRR3579897", "SRX1796665", "SRS1464818", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 6h gill 2", "GSM2176254", null, "source name:gill|tissue:gill|species:zebrafish|replicate:2|time point:6h|temperature:8 degreeC|age:6 mpf", "zebrafish 8 6h gill 2", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "tissue:gill|species:zebrafish|replicate:2|time point:6h|temperature:8 degreeC|age:6 mpf", "GSM2176254", "GSM2176254: zebrafish 8 6h gill 2; Danio rerio; RNA Seq", "GSM2176254", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2176254", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "AZ3.R1.fastq.gz AZ3.R2.fastq.gz", "fastq fastq", 3202950394.0, 14692433.0, "GSM2176254 r1", "0:109 1:109", "A:857599911;C:740206178;G:741631238;T:861040472;N:2472595", 109, 109, null, null, 857599911, 740206178, 741631238, 861040472, 2472595, "SRX1796665", "SRS1464818", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.92927, 0.93296, 0.1223, 0.12211, 0.6801, 0.68189, 0.49864, 0.49957, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-05-24", "Adult", "Adult", "Gill", "Respiratory System"], [39708, "SRR3579896", "SRX1796664", "SRS1464817", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 6h gill 1", "GSM2176253", null, "source name:gill|tissue:gill|species:zebrafish|replicate:1|time point:6h|temperature:8 degreeC|age:6 mpf", "zebrafish 8 6h gill 1", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "tissue:gill|species:zebrafish|replicate:1|time point:6h|temperature:8 degreeC|age:6 mpf", "GSM2176253", "GSM2176253: zebrafish 8 6h gill 1; Danio rerio; RNA Seq", "GSM2176253", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2176253", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "AZ2.R1.fastq.gz AZ2.R2.fastq.gz", "fastq fastq", 3207505722.0, 14713329.0, "GSM2176253 r1", "0:109 1:109", "A:855447431;C:743239876;G:742942682;T:863378143;N:2497590", 109, 109, null, null, 855447431, 743239876, 742942682, 863378143, 2497590, "SRX1796664", "SRS1464817", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.93016, 0.93443, 0.11754, 0.11651, 0.69023, 0.69213, 0.50033, 0.5004, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-05-24", "Adult", "Adult", "Gill", "Respiratory System"], [39709, "SRR3579895", "SRX1796663", "SRS1464816", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 0h gill 3", "GSM2176252", null, "source name:gill|tissue:gill|species:zebrafish|replicate:3|time point:0h|temperature:8 degreeC|age:6 mpf", "zebrafish 8 0h gill 3", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "tissue:gill|species:zebrafish|replicate:3|time point:0h|temperature:8 degreeC|age:6 mpf", "GSM2176252", "GSM2176252: zebrafish 8 0h gill 3; Danio rerio; RNA Seq", "GSM2176252", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2176252", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "AZ1.R1.fastq.gz AZ1.R2.fastq.gz", "fastq fastq", 2657966090.0, 12192505.0, "GSM2176252 r1", "0:109 1:109", "A:707609624;C:618473475;G:616075644;T:713757642;N:2049705", 109, 109, null, null, 707609624, 618473475, 616075644, 713757642, 2049705, "SRX1796663", "SRS1464816", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.93562, 0.9391, 0.0969, 0.09613, 0.68124, 0.68288, 0.49352, 0.48196, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-05-24", "Adult", "Adult", "Gill", "Respiratory System"], [39710, "SRR2067888", "SRX1063367", "SRS963393", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 12h gill 2", "GSM1714084", null, "source name:gill|age:6 months|tissue:gill|group:11|replicate:2|condition:LOE 12h|temperature:8\u00b0C", "zebrafish 8 12h gill 2", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:11|replicate:2|condition:LOE 12h|temperature:8\u00b0C", "GSM1714084", "GSM1714084: zebrafish 8 12h gill 2; Danio rerio; RNA Seq", "GSM1714084", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_LOE_12h_gill_2_2.fq.gz zebrafish_LOE_12h_gill_2_1.fq.gz", "fastq fastq", 3433893272.0, 15751804.0, "GSM1714084 r1", "0:109 1:109", "A:929285053;C:798076747;G:794515113;T:911786961;N:229398", 109, 109, null, null, 929285053, 798076747, 794515113, 911786961, 229398, "SRX1063367", "SRS963393", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.89177, 0.89023, 0.11452, 0.11377, 0.69684, 0.69917, 0.4984, 0.50064, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [39711, "SRR2067887", "SRX1063366", "SRS963395", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 12h gill 1", "GSM1714083", null, "source name:gill|age:6 months|tissue:gill|group:11|replicate:1|condition:LOE 12h|temperature:8\u00b0C", "zebrafish 8 12h gill 1", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:11|replicate:1|condition:LOE 12h|temperature:8\u00b0C", "GSM1714083", "GSM1714083: zebrafish 8 12h gill 1; Danio rerio; RNA Seq", "GSM1714083", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_LOE_12h_gill_1_1.fq.gz zebrafish_LOE_12h_gill_1_2.fq.gz", "fastq fastq", 2809269426.0, 12886557.0, "GSM1714083 r1", "0:109 1:109", "A:746647853;C:662133538;G:660978954;T:739327059;N:182022", 109, 109, null, null, 746647853, 662133538, 660978954, 739327059, 182022, "SRX1063366", "SRS963395", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.90881, 0.90909, 0.10589, 0.10574, 0.69307, 0.69552, 0.49893, 0.4996, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [39712, "SRR2067886", "SRX1063365", "SRS963394", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 0h gill 2", "GSM1714082", null, "source name:gill|age:6 months|tissue:gill|group:10|replicate:2|condition:LOE 0h|temperature:8\u00b0C", "zebrafish 8 0h gill 2", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:10|replicate:2|condition:LOE 0h|temperature:8\u00b0C", "GSM1714082", "GSM1714082: zebrafish 8 0h gill 2; Danio rerio; RNA Seq", "GSM1714082", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_LOE_0h_gill_2_2.fq.gz zebrafish_LOE_0h_gill_2_1.fq.gz", "fastq fastq", 3314206040.0, 15202780.0, "GSM1714082 r1", "0:109 1:109", "A:876309775;C:785596042;G:783767015;T:868315301;N:217907", 109, 109, null, null, 876309775, 785596042, 783767015, 868315301, 217907, "SRX1063365", "SRS963394", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.91374, 0.91359, 0.10013, 0.1009, 0.69112, 0.69353, 0.49181, 0.49578, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [39713, "SRR2067884", "SRX1063364", "SRS963397", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 8 0h gill 1", "GSM1714081", null, "source name:gill|age:6 months|tissue:gill|group:10|replicate:1|condition:LOE 0h|temperature:8\u00b0C", "zebrafish 8 0h gill 1", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:10|replicate:1|condition:LOE 0h|temperature:8\u00b0C", "GSM1714081", "GSM1714081: zebrafish 8 0h gill 1; Danio rerio; RNA Seq", "GSM1714081", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_LOE_0h_gill_1_2.fq.gz zebrafish_LOE_0h_gill_1_1.fq.gz", "fastq fastq", 3365277336.0, 15437052.0, "GSM1714081 r1", "0:109 1:109", "A:886390709;C:799926200;G:799651565;T:879089225;N:219637", 109, 109, null, null, 886390709, 799926200, 799651565, 879089225, 219637, "SRX1063364", "SRS963397", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.91394, 0.91483, 0.09867, 0.09893, 0.68641, 0.68968, 0.49615, 0.49076, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [39714, "SRR2067883", "SRX1063363", "SRS963396", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 28 gill 3", "GSM1714080", null, "source name:gill|age:6 months|tissue:gill|group:9|replicate:3|condition:28\u00b0C|temperature:28\u00b0C", "zebrafish 28 gill 3", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:9|replicate:3|condition:28\u00b0C|temperature:28\u00b0C", "GSM1714080", "GSM1714080: zebrafish 28 gill 3; Danio rerio; RNA Seq", "GSM1714080", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714080", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_28_gill_3_1.fq.gz zebrafish_28_gill_3_2.fq.gz", "fastq fastq", 3254092540.0, 14927030.0, "GSM1714080 r1", "0:109 1:109", "A:858267547;C:771084069;G:771064626;T:853459447;N:216851", 109, 109, null, null, 858267547, 771084069, 771064626, 853459447, 216851, "SRX1063363", "SRS963396", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.90316, 0.90236, 0.08907, 0.08895, 0.67823, 0.6802, 0.49089, 0.49051, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [39715, "SRR2067882", "SRX1063362", "SRS963398", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 28 gill 2", "GSM1714079", null, "source name:gill|age:6 months|tissue:gill|group:9|replicate:2|condition:28\u00b0C|temperature:28\u00b0C", "zebrafish 28 gill 2", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:9|replicate:2|condition:28\u00b0C|temperature:28\u00b0C", "GSM1714079", "GSM1714079: zebrafish 28 gill 2; Danio rerio; RNA Seq", "GSM1714079", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714079", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_28_gill_2_2.fq.gz zebrafish_28_gill_2_1.fq.gz", "fastq fastq", 2621117986.0, 12023477.0, "GSM1714079 r1", "0:109 1:109", "A:690118661;C:623432564;G:622600619;T:684797673;N:168469", 109, 109, null, null, 690118661, 623432564, 622600619, 684797673, 168469, "SRX1063362", "SRS963398", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.90329, 0.90413, 0.08957, 0.09004, 0.67529, 0.67673, 0.49233, 0.49384, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [39716, "SRR2067881", "SRX1063361", "SRS963399", "SRP059605", "PRJNA287283", "Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish", "GSE69965", "Other", "Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28\u00b0C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8\u00b0C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8\u00b0C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.\u00a0 Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia", null, "pubmed:27356472", null, "zebrafish 28 gill 1", "GSM1714078", null, "source name:gill|age:6 months|tissue:gill|group:9|replicate:1|condition:28\u00b0C|temperature:28\u00b0C", "zebrafish 28 gill 1", "Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample", "gill", "Fishes were subjected to a stepped cooling by lowering 1\u00b0C /h to 8\u00b0C and then maintained at 8\u00b0C. When temperature declined to 8\u00b0C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28\u00b0C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq.", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Tilapia and zebrafish were raised and maintained at 28\u00b11\u00b0C in well managed aquariums.", "age:6 months|tissue:gill|group:9|replicate:1|condition:28\u00b0C|temperature:28\u00b0C", "GSM1714078", "GSM1714078: zebrafish 28 gill 1; Danio rerio; RNA Seq", "GSM1714078", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1714078", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP059605", null, null, "zebrafish_28_gill_1_1.fq.gz zebrafish_28_gill_1_2.fq.gz", "fastq fastq", 2867801336.0, 13155052.0, "GSM1714078 r1", "0:109 1:109", "A:765671592;C:675469841;G:688613306;T:737863609;N:182988", 109, 109, null, null, 765671592, 675469841, 688613306, 737863609, 182988, "SRX1063361", "SRS963399", "SRA273258", "GEO", "Shanghai Ocean University", 2, 0.90743, 0.9075, 0.08734, 0.08732, 0.68158, 0.68199, 0.48076, 0.4913, 109, 109, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2015-06-17", "Adult", "Adult", "Gill", "Respiratory System"], [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.", null, "pubmed:34660600", null, "Gill6", "GSM5924279", null, "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", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:gill|genotype:wild type", "GSM5924279", "GSM5924279: Gill6; Danio rerio; RNA Seq", "GSM5924279", null, "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", null, "SRP194254", null, "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, null, null, 5239766235, 3329504882, 3343228185, 7895078269, 2368029, "SRX14328405", "SRS12144036", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.70563, 0.0, 0.05162, 1.0, 0.8565, null, 0.67358, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gill", "Respiratory System"], [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.", null, "pubmed:34660600", null, "Gill5", "GSM5924278", null, "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", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:gill|genotype:wild type", "GSM5924278", "GSM5924278: Gill5; Danio rerio; RNA Seq", "GSM5924278", null, "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", null, "SRP194254", null, "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, null, null, 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", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gill", "Respiratory System"], [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.", null, "pubmed:34660600", null, "Gill3", "GSM5924277", null, "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", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:gill|genotype:wild type", "GSM5924277", "GSM5924277: Gill3; Danio rerio; RNA Seq", "GSM5924277", null, "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", null, "SRP194254", null, "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, null, null, 5441997035, 3521528250, 3625669551, 8988770258, 1857806, "SRX14328403", "SRS12144034", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.74255, 0.0, 0.03463, 1.0, 0.81434, null, 0.586, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2022-03-01", "Undetermined", "Multi-stage", "Gill", "Respiratory System"], [60514, "SRR12340121", "SRX8839908", "SRS7103142", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill DsRedx 3", "GSM4698505", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill DsRedx 3", "Raw reads were first aligned to zebrafish reference genome danRer11\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698505", "GSM4698505: sox17 gill DsRedx 3; Danio rerio; RNA Seq", "GSM4698505", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698505", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_DsRedx_3_R1.fq.gz sox17_gill_DsRedx_3_R2.fq.gz", "fastq fastq", 6482204823.0, 22206962.0, "GSM4698505 r1", "0:146.24 1:145.66", "A:1892664132;C:1333446985;G:1270670352;T:1985394285;N:29069", 146, 145, null, null, 1892664132, 1333446985, 1270670352, 1985394285, 29069, "SRX8839908", "SRS7103142", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.79891, 0.79555, 0.23795, 0.23516, 0.886, 0.88613, 0.48969, 0.48724, 150, 148, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60515, "SRR12340120", "SRX8839907", "SRS7103140", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill DsRedx 2", "GSM4698504", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill DsRedx 2", "Raw reads were first aligned to zebrafish reference genome danRer11\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698504", "GSM4698504: sox17 gill DsRedx 2; Danio rerio; RNA Seq", "GSM4698504", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698504", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_DsRedx_2_R1.fq.gz sox17_gill_DsRedx_2_R2.fq.gz", "fastq fastq", 6871522969.0, 23718551.0, "GSM4698504 r1", "0:145.07 1:144.64", "A:1996597634;C:1433447769;G:1330303568;T:2111142421;N:31577", 145, 144, null, null, 1996597634, 1433447769, 1330303568, 2111142421, 31577, "SRX8839907", "SRS7103140", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.77789, 0.77647, 0.23871, 0.23784, 0.90319, 0.90402, 0.59462, 0.59357, 149, 80, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60516, "SRR12340119", "SRX8839906", "SRS7103139", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill DsRedx 1", "GSM4698503", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill DsRedx 1", "Raw reads were first aligned to zebrafish reference genome danRer11\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698503", "GSM4698503: sox17 gill DsRedx 1; Danio rerio; RNA Seq", "GSM4698503", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698503", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_DsRedx_1_R1.fq.gz sox17_gill_DsRedx_1_R2.fq.gz", "fastq fastq", 6640801871.0, 23132663.0, "GSM4698503 r1", "0:143.42 1:143.65", "A:1787496811;C:1555982056;G:1401318306;T:1895972742;N:31956", 143, 143, null, null, 1787496811, 1555982056, 1401318306, 1895972742, 31956, "SRX8839906", "SRS7103139", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.82205, 0.82023, 0.17657, 0.17516, 0.88799, 0.88846, 0.60101, 0.5999, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60517, "SRR12340118", "SRX8839905", "SRS7103141", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill GFP 3", "GSM4698502", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill GFP 3", "Raw reads were first aligned to zebrafish reference genome danRer11\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698502", "GSM4698502: sox17 gill GFP 3; Danio rerio; RNA Seq", "GSM4698502", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698502", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_GFP_3_R1.fq.gz sox17_gill_GFP_3_R2.fq.gz", "fastq fastq", 5881408853.0, 20262087.0, "GSM4698502 r1", "0:145.09 1:145.18", "A:1611164278;C:1359776238;G:1263385328;T:1647055163;N:27846", 145, 145, null, null, 1611164278, 1359776238, 1263385328, 1647055163, 27846, "SRX8839905", "SRS7103141", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.85631, 0.85552, 0.14127, 0.14135, 0.88972, 0.89065, 0.53836, 0.53645, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60518, "SRR12340117", "SRX8839904", "SRS7103138", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill GFP 2", "GSM4698501", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill GFP 2", "Raw reads were first aligned to zebrafish reference genome danRer11\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698501", "GSM4698501: sox17 gill GFP 2; Danio rerio; RNA Seq", "GSM4698501", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698501", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_GFP_2_R1.fq.gz sox17_gill_GFP_2_R2.fq.gz", "fastq fastq", 6629269698.0, 23040040.0, "GSM4698501 r1", "0:143.67 1:144.06", "A:1792321281;C:1562626172;G:1410652523;T:1863639213;N:30509", 143, 144, null, null, 1792321281, 1562626172, 1410652523, 1863639213, 30509, "SRX8839904", "SRS7103138", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.87337, 0.87168, 0.16298, 0.16158, 0.86563, 0.86582, 0.57739, 0.58009, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [60519, "SRR12340116", "SRX8839903", "SRS7103137", "SRP273975", "PRJNA649247", "Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine", "GSE155287", "Transcriptome Analysis", "In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "pubmed:33027664", null, "sox17 gill GFP 1", "GSM4698500", null, "source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "sox17 gill GFP 1", "Raw reads were first aligned to zebrafish reference genome danRer11\u00a0using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample", "specific cells types in zebrafish gill", null, "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", null, "tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP", "GSM4698500", "GSM4698500: sox17 gill GFP 1; Danio rerio; RNA Seq", "GSM4698500", null, "1", "30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.", "GEO Accession:GSM4698500", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP273975", null, null, "sox17_gill_GFP_1_R1.fq.gz sox17_gill_GFP_1_R2.fq.gz", "fastq fastq", 8550712115.0, 29745129.0, "GSM4698500 r1", "0:143.49 1:143.98", "A:2279816799;C:2045513877;G:1883280335;T:2342060508;N:40596", 143, 143, null, null, 2279816799, 2045513877, 1883280335, 2342060508, 40596, "SRX8839903", "SRS7103137", "SRA1104756", "GEO", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.87481, 0.87331, 0.14783, 0.14775, 0.84824, 0.84946, 0.54943, 0.47083, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-07-28", "Adult", "Adult", "Gill", "Respiratory System"], [61563, 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