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260 rows where experiment.library_layout = "PAIRED" and tissue_curation_coarse = "Respiratory System"

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experiment.library_selection 8

technology 4

devstage_curation_coarse 4

devstage_curation 3

experiment.platform 2

experiment.library_source 2

tissue_curation_coarse 1

  • Respiratory System · 260 ✖

tissue_curation 1

experiment.library_strategy 1

experiment.library_layout 1

  • PAIRED · 260 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
240 240 DRR162501 DRX153120 DRS083181 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.       gill sample from 39 mpf zebrafish replicate5 SAMD00152449   sample name:g39 5|age:39 month|biological replicate:5|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152449 DRX153120 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152449       871964800.0 4359824.0 DRR162501 0:100 1:100 A:245477085;C:190759033;G:191262929;T:244420643;N:45110 100 100     245477085 190759033 191262929 244420643 45110 DRX153120 DRS083181 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 0.91962 0.91237 0.09868 0.09688 0.71161 0.71307 0.53167 0.51753 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
241 241 DRR162500 DRX153119 DRS083180 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.       gill sample from 39 mpf zebrafish replicate4 SAMD00152448   sample name:g39 4|age:39 month|biological replicate:4|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152448 DRX153119 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152448       1034286600.0 5171433.0 DRR162500 0:100 1:100 A:298325965;C:219665025;G:219344349;T:296896484;N:54777 100 100     298325965 219665025 219344349 296896484 54777 DRX153119 DRS083180 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 0.91301 0.90076 0.11123 0.10834 0.70778 0.71165 0.55555 0.56161 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
242 242 DRR162499 DRX153118 DRS083179 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.       gill sample from 39 mpf zebrafish replicate3 SAMD00152447   sample name:g39 3|age:39 month|biological replicate:3|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152447 DRX153118 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152447       992791600.0 4963958.0 DRR162499 0:100 1:100 A:282861329;C:214120789;G:214176850;T:281583783;N:48849 100 100     282861329 214120789 214176850 281583783 48849 DRX153118 DRS083179 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 0.91255 0.90373 0.11243 0.11 0.69852 0.70088 0.51884 0.51758 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
243 243 DRR162498 DRX153117 DRS083178 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.       gill sample from 39 mpf zebrafish replicate2 SAMD00152446   sample name:g39 2|age:39 month|biological replicate:2|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152446 DRX153117 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152446       1080763400.0 5403817.0 DRR162498 0:100 1:100 A:302043911;C:238927150;G:239803992;T:299932712;N:55635 100 100     302043911 238927150 239803992 299932712 55635 DRX153117 DRS083178 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 0.91984 0.90678 0.10184 0.09991 0.70414 0.70646 0.53712 0.52438 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
244 244 DRR162497 DRX153116 DRS083177 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.       gill sample from 39 mpf zebrafish replicate1 SAMD00152445   sample name:g39 1|age:39 month|biological replicate:1|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152445 DRX153116 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152445       820518000.0 4102590.0 DRR162497 0:100 1:100 A:231130129;C:179223787;G:180371594;T:229751631;N:40859 100 100     231130129 179223787 180371594 229751631 40859 DRX153116 DRS083177 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 0.91577 0.90267 0.09839 0.09587 0.69307 0.69609 0.48968 0.52952 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
245 245 DRR162496 DRX153115 DRS083176 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.       gill sample from 16 mpf zebrafish replicate5 SAMD00152444   sample name:g16 5|age:16 month|biological replicate:5|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152444 DRX153115 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152444       1102199600.0 5510998.0 DRR162496 0:100 1:100 A:305265016;C:246727253;G:250574196;T:299577567;N:55568 100 100     305265016 246727253 250574196 299577567 55568 DRX153115 DRS083176 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 0.95268 0.93003 0.06876 0.0661 0.77727 0.78135 0.5295 0.56032 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
246 246 DRR162495 DRX153114 DRS083175 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.       gill sample from 16 mpf zebrafish replicate4 SAMD00152443   sample name:g16 4|age:16 month|biological replicate:4|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152443 DRX153114 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152443       982848600.0 4914243.0 DRR162495 0:100 1:100 A:282893187;C:208838989;G:210075565;T:280991626;N:49233 100 100     282893187 208838989 210075565 280991626 49233 DRX153114 DRS083175 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 0.91267 0.89935 0.10283 0.10062 0.70437 0.7095 0.53489 0.54118 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
247 247 DRR162494 DRX153113 DRS083174 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.       gill sample from 16 mpf zebrafish replicate3 SAMD00152442   sample name:g16 3|age:16 month|biological replicate:3|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152442 DRX153113 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152442       1016621200.0 5083106.0 DRR162494 0:100 1:100 A:279935742;C:228896828;G:231468225;T:276269198;N:51207 100 100     279935742 228896828 231468225 276269198 51207 DRX153113 DRS083174 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 0.95111 0.93887 0.08748 0.08497 0.69623 0.69952 0.52937 0.59843 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
248 248 DRR162493 DRX153112 DRS083173 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.       gill sample from 16 mpf zebrafish replicate2 SAMD00152441   sample name:g16 2|age:16 month|biological replicate:2|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152441 DRX153112 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152441       722304200.0 3611521.0 DRR162493 0:100 1:100 A:200278892;C:161158001;G:162331081;T:198500131;N:36095 100 100     200278892 161158001 162331081 198500131 36095 DRX153112 DRS083173 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 0.93204 0.92019 0.10234 0.1011 0.69298 0.69725 0.51924 0.51355 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
249 249 DRR162492 DRX153111 DRS083172 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.       gill sample from 16 mpf zebrafish replicate1 SAMD00152440   sample name:g16 1|age:16 month|biological replicate:1|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152440 DRX153111 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152440       931454400.0 4657272.0 DRR162492 0:100 1:100 A:263779492;C:202289539;G:203757307;T:261579177;N:48885 100 100     263779492 202289539 203757307 261579177 48885 DRX153111 DRS083172 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 0.92078 0.90904 0.11618 0.11402 0.69972 0.70276 0.5257 0.51912 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
250 250 DRR162491 DRX153110 DRS083171 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.       gill sample from 7 mpf zebrafish replicate5 SAMD00152439   sample name:g07 5|age:7 month|biological replicate:5|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152439 DRX153110 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152439       784719200.0 3923596.0 DRR162491 0:100 1:100 A:208600449;C:184617145;G:185368380;T:206094627;N:38599 100 100     208600449 184617145 185368380 206094627 38599 DRX153110 DRS083171 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 0.92664 0.91688 0.08725 0.08595 0.7049 0.71792 0.53669 0.53755 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
251 251 DRR162490 DRX153109 DRS083170 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.       gill sample from 7 mpf zebrafish replicate4 SAMD00152438   sample name:g07 4|age:7 month|biological replicate:4|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152438 DRX153109 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152438       850741800.0 4253709.0 DRR162490 0:100 1:100 A:238671193;C:187142318;G:188600377;T:236285874;N:42038 100 100     238671193 187142318 188600377 236285874 42038 DRX153109 DRS083170 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 0.92289 0.90779 0.10939 0.10663 0.69432 0.69763 0.52938 0.52843 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Gill Respiratory System
252 252 DRR162489 DRX153108 DRS083169 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.       gill sample from 7 mpf zebrafish replicate3 SAMD00152437   sample name:g07 3|age:7 month|biological replicate:3|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152437 DRX153108 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152437       1104355400.0 5521777.0 DRR162489 0:100 1:100 A:293305974;C:258987844;G:260252632;T:291752232;N:56718 100 100     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   Japan 2018-12-24 Adult Adult Gill Respiratory System
253 253 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.       gill sample from 7 mpf zebrafish replicate2 SAMD00152436   sample name:g07 2|age:7 month|biological replicate:2|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152436 DRX153107 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152436       843955600.0 4219778.0 DRR162488 0:100 1:100 A:223801058;C:198393089;G:199123839;T:222593773;N:43841 100 100     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   Japan 2018-12-24 Adult Adult Gill Respiratory System
254 254 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.       gill sample from 7 mpf zebrafish replicate1 SAMD00152435   sample name:g07 1|age:7 month|biological replicate:1|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152435 DRX153106 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152435       910082000.0 4550410.0 DRR162487 0:100 1:100 A:241668250;C:213411555;G:214645944;T:240311041;N:45210 100 100     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   Japan 2018-12-24 Adult Adult Gill Respiratory System
255 255 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.       gill sample from 2 mpf zebrafish replicate5 SAMD00152434   sample name:g02 5|age:2 month|biological replicate:5|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152434 DRX153105 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152434       1270126600.0 6350633.0 DRR162486 0:100 1:100 A:342076596;C:293249973;G:295429735;T:339306175;N:64121 100 100     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   Japan 2018-12-24 Juvenile Juvenile Gill Respiratory System
256 256 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.       gill sample from 2 mpf zebrafish replicate4 SAMD00152433   sample name:g02 4|age:2 month|biological replicate:4|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152433 DRX153104 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152433       835205000.0 4176025.0 DRR162485 0:100 1:100 A:224993396;C:192858928;G:193779680;T:223531224;N:41772 100 100     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   Japan 2018-12-24 Juvenile Juvenile Gill Respiratory System
257 257 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.       gill sample from 2 mpf zebrafish replicate3 SAMD00152432   sample name:g02 3|age:2 month|biological replicate:3|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152432 DRX153103 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152432       1038999000.0 5194995.0 DRR162484 0:100 1:100 A:278673674;C:241111198;G:242737620;T:276422623;N:53885 100 100     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   Japan 2018-12-24 Juvenile Juvenile Gill Respiratory System
258 258 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.       gill sample from 2 mpf zebrafish replicate2 SAMD00152431   sample name:g02 2|age:2 month|biological replicate:2|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152431 DRX153102 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152431       632886400.0 3164432.0 DRR162483 0:100 1:100 A:169214113;C:147628963;G:147454557;T:168556741;N:32026 100 100     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   Japan 2018-12-24 Juvenile Juvenile Gill Respiratory System
259 259 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.       gill sample from 2 mpf zebrafish replicate1 SAMD00152430   sample name:g02 1|age:2 month|biological replicate:1|tissue:gill                 Illumina HiSeq 2000 paired end sequencing of SAMD00152430 DRX153101 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152430       1323105600.0 6615528.0 DRR162482 0:100 1:100 A:355611103;C:306237205;G:307478272;T:353712733;N:66287 100 100     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   Japan 2018-12-24 Juvenile Juvenile Gill Respiratory System
9842 9842 ERR4029259 ERX4030575 ERS4514128 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 4 SAMEA6786449 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786449|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 4|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 4 p Sample 4 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB4_S41_R1_001.fastq.gz FB4_S41_R2_001.fastq.gz fastq fastq 4354809436.0 29071030.0 E MTAB 8958:FB4 S41 R 0:74.90 1:74.90 A:1140431810;C:1005396495;G:1008528915;T:1171220102;N:29232114 74 74     1140431810 1005396495 1008528915 1171220102 29232114 ERX4030575 ERS4514128 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91143 0.91076 0.10123 0.09941 0.68235 0.68452 0.48713 0.48998 76 74 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9843 9843 ERR4029258 ERX4030574 ERS4514127 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 3 SAMEA6786448 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786448|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 3|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 3 p Sample 3 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB3_S40_R1_001.fastq.gz FB3_S40_R2_001.fastq.gz fastq fastq 3973860397.0 26559713.0 E MTAB 8958:FB3 S40 R 0:74.80 1:74.82 A:1038749031;C:917944667;G:920080717;T:1066160216;N:30925766 74 74     1038749031 917944667 920080717 1066160216 30925766 ERX4030574 ERS4514127 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91065 0.90981 0.10133 0.09911 0.68789 0.68945 0.47182 0.49996 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9844 9844 ERR4029257 ERX4030573 ERS4514126 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 2 SAMEA6786447 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786447|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 2|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 2 p Sample 2 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB2_S39_R1_001.fastq.gz FB2_S39_R2_001.fastq.gz fastq fastq 4135184845.0 27517010.0 E MTAB 8958:FB2 S39 R 0:75.15 1:75.13 A:1084253902;C:962303819;G:961163738;T:1111949967;N:15513419 75 75     1084253902 962303819 961163738 1111949967 15513419 ERX4030573 ERS4514126 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91098 0.91057 0.09468 0.09311 0.68095 0.68282 0.49982 0.50146 75 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9845 9845 ERR4029256 ERX4030572 ERS4514125 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 1 SAMEA6786446 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786446|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 1|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 1 p Sample 1 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 06 17 FB1_S38_R1_001.fastq FB1_S38_R2_001.fastq fastq fastq 4651073045.0 31021879.0 E MTAB 8958:FB1 S38 R 0:74.96 1:74.97 A:1225305023;C:1072643957;G:1069905162;T:1255950159;N:27268744 74 74     1225305023 1072643957 1069905162 1255950159 27268744 ERX4030572 ERS4514125 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91441 0.91282 0.10095 0.09913 0.686 0.68745 0.49433 0.5047 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9846 9846 ERR4029255 ERX4030571 ERS4514124 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 16 SAMEA6786445 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786445|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 16|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 16|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 16 p Sample 16 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB4_S20_R1_001.fastq.gz FB4_S20_R2_001.fastq.gz fastq fastq 5961540086.0 39717871.0 E MTAB 8958:FB4 S20 R 0:75.07 1:75.03 A:1565483441;C:1390303898;G:1372759826;T:1611361282;N:21631639 75 75     1565483441 1390303898 1372759826 1611361282 21631639 ERX4030571 ERS4514124 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90959 0.90989 0.0925 0.09172 0.68787 0.68929 0.49093 0.49057 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9847 9847 ERR4029254 ERX4030570 ERS4514123 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 15 SAMEA6786444 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786444|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 15|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 15|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 15 p Sample 15 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB3_S19_R1_001.fastq.gz FB3_S19_R2_001.fastq.gz fastq fastq 6835575760.0 45515064.0 E MTAB 8958:FB3 S19 R 0:75.11 1:75.07 A:1802176562;C:1589590146;G:1564279107;T:1858606235;N:20923710 75 75     1802176562 1589590146 1564279107 1858606235 20923710 ERX4030570 ERS4514123 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90945 0.91123 0.09519 0.09378 0.67963 0.67961 0.49246 0.49476 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9848 9848 ERR4029253 ERX4030569 ERS4514122 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 14 SAMEA6786443 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786443|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 14|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 14|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 14 p Sample 14 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB2_S18_R1_001.fastq.gz FB2_S18_R2_001.fastq.gz fastq fastq 5789923311.0 38517674.0 E MTAB 8958:FB2 S18 R 0:75.18 1:75.14 A:1520250885;C:1354960735;G:1336204150;T:1565011084;N:13496457 75 75     1520250885 1354960735 1336204150 1565011084 13496457 ERX4030569 ERS4514122 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91863 0.91917 0.08923 0.08753 0.68848 0.68883 0.5042 0.50799 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9849 9849 ERR4029252 ERX4030568 ERS4514121 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 13 SAMEA6786442 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786442|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 13|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 13|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 13 p Sample 13 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB1_S17_R1_001.fastq.gz FB1_S17_R2_001.fastq.gz fastq fastq 6951804793.0 46295025.0 E MTAB 8958:FB1 S17 R 0:75.10 1:75.06 A:1827618209;C:1618955946;G:1595802123;T:1884739421;N:24689094 75 75     1827618209 1618955946 1595802123 1884739421 24689094 ERX4030568 ERS4514121 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90991 0.90972 0.09297 0.09193 0.68284 0.68392 0.49878 0.5017 74 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9850 9850 ERR4029251 ERX4030567 ERS4514120 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 20 SAMEA6786441 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786441|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 20|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 20|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 20 p Sample 20 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB4_S44_R1_001.fastq.gz FB4_S44_R2_001.fastq.gz fastq fastq 9629684100.0 64667395.0 E MTAB 8958:FB4 S44 R 0:74.47 1:74.44 A:2552333346;C:2176006333;G:2180111416;T:2614191329;N:107041676 74 74     2552333346 2176006333 2180111416 2614191329 107041676 ERX4030567 ERS4514120 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90795 0.90756 0.10044 0.09789 0.6888 0.69256 0.50043 0.4932 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9851 9851 ERR4029250 ERX4030566 ERS4514119 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 19 SAMEA6786440 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786440|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 19|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 19|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 19 p Sample 19 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB3_S43_R1_001.fastq.gz FB3_S43_R2_001.fastq.gz fastq fastq 11268744444.0 75088756.0 E MTAB 8958:FB3 S43 R 0:75.06 1:75.01 A:2983863814;C:2608268633;G:2555098938;T:3072413168;N:49099891 75 75     2983863814 2608268633 2555098938 3072413168 49099891 ERX4030566 ERS4514119 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.9107 0.91089 0.09522 0.09428 0.69187 0.69266 0.49302 0.49463 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9852 9852 ERR4029249 ERX4030565 ERS4514118 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 18 SAMEA6786439 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786439|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 18|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 18|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 18 p Sample 18 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB2_S42_R1_001.fastq.gz FB2_S42_R2_001.fastq.gz fastq fastq 10434072067.0 69530304.0 E MTAB 8958:FB2 S42 R 0:75.06 1:75.01 A:2749500618;C:2426208950;G:2375421255;T:2834879202;N:48062042 75 75     2749500618 2426208950 2375421255 2834879202 48062042 ERX4030565 ERS4514118 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.9084 0.90779 0.0926 0.0917 0.68809 0.68864 0.49817 0.49902 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9853 9853 ERR4029248 ERX4030564 ERS4514117 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 17 SAMEA6786438 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786438|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 17|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 17|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 17 p Sample 17 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB1_S41_R1_001.fastq.gz FB1_S41_R2_001.fastq.gz fastq fastq 12125040750.0 80781224.0 E MTAB 8958:FB1 S41 R 0:75.08 1:75.02 A:3129480022;C:2890038396;G:2819859086;T:3233228646;N:52434600 75 75     3129480022 2890038396 2819859086 3233228646 52434600 ERX4030564 ERS4514117 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91384 0.91301 0.10967 0.10615 0.69006 0.69041 0.51643 0.51985 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9854 9854 ERR4029247 ERX4030563 ERS4514116 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 8 SAMEA6786437 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786437|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 8|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 8 p Sample 8 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB12_S49_R1_001.fastq.gz FB12_S49_R2_001.fastq.gz fastq fastq 4223131851.0 28165494.0 E MTAB 8958:FB12 S49 R 0:74.95 1:74.99 A:1121514270;C:962554300;G:967294488;T:1146544647;N:25224146 74 74     1121514270 962554300 967294488 1146544647 25224146 ERX4030563 ERS4514116 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91639 0.91413 0.10604 0.10326 0.68162 0.68458 0.49921 0.50172 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9855 9855 ERR4029246 ERX4030562 ERS4514115 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 7 SAMEA6786436 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786436|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 7|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 7 p Sample 7 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB11_S48_R1_001.fastq.gz FB11_S48_R2_001.fastq.gz fastq fastq 4670407305.0 31054128.0 E MTAB 8958:FB11 S48 R 0:75.20 1:75.19 A:1234494738;C:1078360233;G:1084251975;T:1258088405;N:15211954 75 75     1234494738 1078360233 1084251975 1258088405 15211954 ERX4030562 ERS4514115 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.92228 0.92038 0.09418 0.09222 0.68674 0.68862 0.48948 0.48842 75 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9856 9856 ERR4029245 ERX4030561 ERS4514114 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 6 SAMEA6786435 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786435|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 6|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 6 p Sample 6 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB10_S47_R1_001.fastq.gz FB10_S47_R2_001.fastq.gz fastq fastq 3970723047.0 26597167.0 E MTAB 8958:FB10 S47 R 0:74.63 1:74.66 A:1037861230;C:915437247;G:922979694;T:1056625196;N:37819680 74 74     1037861230 915437247 922979694 1056625196 37819680 ERX4030561 ERS4514114 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.92474 0.92246 0.0934 0.0916 0.69106 0.69384 0.49058 0.48154 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9857 9857 ERR4029244 ERX4030560 ERS4514113 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 5 SAMEA6786434 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786434|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 5|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 5 p Sample 5 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB9_S46_R1_001.fastq.gz FB9_S46_R2_001.fastq.gz fastq fastq 4267946165.0 28455064.0 E MTAB 8958:FB9 S46 R 0:75.00 1:74.99 A:1108310330;C:999732020;G:987857724;T:1148193980;N:23852111 75 74     1108310330 999732020 987857724 1148193980 23852111 ERX4030560 ERS4514113 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.9223 0.91737 0.09304 0.09006 0.69063 0.6929 0.48978 0.49675 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9858 9858 ERR4029243 ERX4030559 ERS4514112 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 9 SAMEA6786433 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786433|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 9|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 9 p Sample 9 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB17_S54_R1_001.fastq.gz FB17_S54_R2_001.fastq.gz fastq fastq 3847723303.0 25764874.0 E MTAB 8958:FB17 S54 R 0:74.65 1:74.69 A:1009950686;C:883047473;G:885821368;T:1035313325;N:33590451 74 74     1009950686 883047473 885821368 1035313325 33590451 ERX4030559 ERS4514112 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91088 0.90785 0.09899 0.09623 0.68822 0.69055 0.48686 0.49337 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9859 9859 ERR4029242 ERX4030558 ERS4514111 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 12 SAMEA6786432 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786432|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 12|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 12 p Sample 12 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB20_S57_R1_001.fastq.gz FB20_S57_R2_001.fastq.gz fastq fastq 4534822065.0 30209756.0 E MTAB 8958:FB20 S57 R 0:75.06 1:75.06 A:1181838544;C:1056097162;G:1066594521;T:1207484216;N:22807622 75 75     1181838544 1056097162 1066594521 1207484216 22807622 ERX4030558 ERS4514111 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91577 0.91513 0.09598 0.09473 0.68931 0.69132 0.49181 0.49786 74 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9860 9860 ERR4029241 ERX4030557 ERS4514110 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 11 SAMEA6786431 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786431|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 11|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 11|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 11 p Sample 11 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB19_S56_R1_001.fastq.gz FB19_S56_R2_001.fastq.gz fastq fastq 5070571422.0 33987501.0 E MTAB 8958:FB19 S56 R 0:74.58 1:74.61 A:1327496786;C:1163563377;G:1162870630;T:1365191685;N:51448944 74 74     1327496786 1163563377 1162870630 1365191685 51448944 ERX4030557 ERS4514110 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91091 0.91003 0.09944 0.09748 0.68745 0.69016 0.49706 0.49287 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9861 9861 ERR4029240 ERX4030556 ERS4514109 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 10 SAMEA6786430 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786430|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 10|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 10 p Sample 10 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB18_S55_R1_001.fastq.gz FB18_S55_R2_001.fastq.gz fastq fastq 4411576023.0 29389076.0 E MTAB 8958:FB18 S55 R 0:75.05 1:75.06 A:1153821133;C:1024593137;G:1029312154;T:1181989770;N:21859829 75 75     1153821133 1024593137 1029312154 1181989770 21859829 ERX4030556 ERS4514109 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90933 0.90999 0.09581 0.09404 0.68917 0.69199 0.49527 0.49791 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
19143 19143 ERR14086559 ERX13488933 ERS21188923 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F2 T2 ZF Con 72h F2 T2 SAMEA116144982 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F2 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:221 27805 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F2_T2.pair1.truncated ZF_Con_72h_F2_T2.pair2.truncated fastq fastq 10806719947.0 36110242.0 ena RUN TAB 19 12 2024 10:07:07:222 27806 0:149.64 1:149.64 A:2965060471;C:2438948465;G:2454160636;T:2948358895;N:191480 149 149     2965060471 2438948465 2454160636 2948358895 191480 ERX13488933 ERS21188923 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19144 19144 ERR14086546 ERX13488920 ERS21188910 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F2 T1 ZF Con 2h F2 T1 SAMEA116144969 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F2 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:206 27779 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F2_T1.pair1.truncated ZF_Con_2h_F2_T1.pair2.truncated fastq fastq 14857999358.0 49760457.0 ena RUN TAB 19 12 2024 10:07:07:207 27780 0:149.30 1:149.29 A:4063197170;C:3359903309;G:3389720319;T:4045034265;N:144295 149 149     4063197170 3359903309 3389720319 4045034265 144295 ERX13488920 ERS21188910 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19145 19145 ERR14086581 ERX13488955 ERS21188945 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F2 T1 ZF Inf 72h F2 T1 SAMEA116145004 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F2 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F2 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:243 27849 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F2_T1.pair1.truncated ZF_Inf_72h_F2_T1.pair2.truncated fastq fastq 13688478236.0 45721242.0 ena RUN TAB 19 12 2024 10:07:07:244 27850 0:149.69 1:149.69 A:3754535055;C:3089295285;G:3114000296;T:3730455705;N:191895 149 149     3754535055 3089295285 3114000296 3730455705 191895 ERX13488955 ERS21188945 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19146 19146 ERR14086540 ERX13488914 ERS21188904 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F1 T2 ZF Con 24h F1 T2 SAMEA116144963 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F1 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F1 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:199 27767 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F1_T2.pair1.truncated ZF_Con_24h_F1_T2.pair2.truncated fastq fastq 10450579058.0 34942794.0 ena RUN TAB 19 12 2024 10:07:07:200 27768 0:149.54 1:149.54 A:2875878023;C:2351334168;G:2367670600;T:2855687426;N:8841 149 149     2875878023 2351334168 2367670600 2855687426 8841 ERX13488914 ERS21188904 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19147 19147 ERR14086555 ERX13488929 ERS21188919 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F5 T1 ZF Con 48h F5 T1 SAMEA116144978 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F5 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:216 27797 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F5_T1.pair1.truncated ZF_Con_48h_F5_T1.pair2.truncated fastq fastq 12970550968.0 43346641.0 ena RUN TAB 19 12 2024 10:07:07:217 27798 0:149.61 1:149.61 A:3556627514;C:2927267468;G:2954512353;T:3531914408;N:229225 149 149     3556627514 2927267468 2954512353 3531914408 229225 ERX13488929 ERS21188919 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19148 19148 ERR14086548 ERX13488922 ERS21188912 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F3 T1 ZF Con 2h F3 T1 SAMEA116144971 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F3 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F3 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:208 27783 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F3_T1.pair1.truncated ZF_Con_2h_F3_T1.pair2.truncated fastq fastq 9796047940.0 32778493.0 ena RUN TAB 19 12 2024 10:07:07:209 27784 0:149.43 1:149.43 A:2712516144;C:2185151856;G:2203905915;T:2694465752;N:8273 149 149     2712516144 2185151856 2203905915 2694465752 8273 ERX13488922 ERS21188912 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19149 19149 ERR14086576 ERX13488950 ERS21188940 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F2 T1 ZF Inf 48h F2 T1 SAMEA116144999 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F2 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F2 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27839 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F2_T1.pair1.truncated ZF_Inf_48h_F2_T1.pair2.truncated fastq fastq 10400268770.0 34736762.0 ena RUN TAB 19 12 2024 10:07:07:239 27840 0:149.70 1:149.70 A:2850649951;C:2367895411;G:2362604415;T:2819029152;N:89841 149 149     2850649951 2367895411 2362604415 2819029152 89841 ERX13488950 ERS21188940 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19150 19150 ERR14086580 ERX13488954 ERS21188944 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F5 T2 ZF Inf 48h F5 T2 SAMEA116145003 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F5 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:242 27847 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F5_T2.pair1.truncated ZF_Inf_48h_F5_T2.pair2.truncated fastq fastq 11541953511.0 38615622.0 ena RUN TAB 19 12 2024 10:07:07:243 27848 0:149.45 1:149.45 A:3149621954;C:2617992293;G:2634267865;T:3139910090;N:161309 149 149     3149621954 2617992293 2634267865 3139910090 161309 ERX13488954 ERS21188944 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19151 19151 ERR14086547 ERX13488921 ERS21188911 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F2 T2 ZF Con 2h F2 T2 SAMEA116144970 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F2 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:207 27781 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F2_T2.pair1.truncated ZF_Con_2h_F2_T2.pair2.truncated fastq fastq 13863272461.0 46344391.0 ena RUN TAB 19 12 2024 10:07:07:208 27782 0:149.57 1:149.57 A:3792400588;C:3136237717;G:3165201062;T:3769186938;N:246156 149 149     3792400588 3136237717 3165201062 3769186938 246156 ERX13488921 ERS21188911 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19152 19152 ERR14086550 ERX13488924 ERS21188914 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F5 T2 ZF Con 2h F5 T2 SAMEA116144973 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F5 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:210 27787 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F5_T2.pair1.truncated ZF_Con_2h_F5_T2.pair2.truncated fastq fastq 12875582522.0 43072753.0 ena RUN TAB 19 12 2024 10:07:07:211 27788 0:149.46 1:149.46 A:3497197102;C:2940877881;G:2959759457;T:3477623582;N:124500 149 149     3497197102 2940877881 2959759457 3477623582 124500 ERX13488924 ERS21188914 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19153 19153 ERR14086586 ERX13488960 ERS21188950 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F7 T2 ZF Inf 72h F7 T2 SAMEA116145009 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F7 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F7 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:248 27859 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F7_T2.pair1.truncated ZF_Inf_72h_F7_T2.pair2.truncated fastq fastq 13295980347.0 44467065.0 ena RUN TAB 19 12 2024 10:07:07:249 27860 0:149.50 1:149.50 A:3621424205;C:3027543860;G:3042454743;T:3604321654;N:235885 149 149     3621424205 3027543860 3042454743 3604321654 235885 ERX13488960 ERS21188950 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19154 19154 ERR14086561 ERX13488935 ERS21188925 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F4 T1 ZF Con 72h F4 T1 SAMEA116144984 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F4 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F4 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:224 27809 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F4_T1.pair1.truncated ZF_Con_72h_F4_T1.pair2.truncated fastq fastq 9938081497.0 33212946.0 ena RUN TAB 19 12 2024 10:07:07:224 27810 0:149.61 1:149.61 A:2721489962;C:2248630062;G:2262566481;T:2705255710;N:139282 149 149     2721489962 2248630062 2262566481 2705255710 139282 ERX13488935 ERS21188925 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19155 19155 ERR14086579 ERX13488953 ERS21188943 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F5 T1 ZF Inf 48h F5 T1 SAMEA116145002 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F5 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:241 27845 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F5_T1.pair1.truncated ZF_Inf_48h_F5_T1.pair2.truncated fastq fastq 12222927812.0 40990200.0 ena RUN TAB 19 12 2024 10:07:07:242 27846 0:149.10 1:149.10 A:3396661594;C:2718183404;G:2739192225;T:3368673043;N:217546 149 149     3396661594 2718183404 2739192225 3368673043 217546 ERX13488953 ERS21188943 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19156 19156 ERR14086573 ERX13488947 ERS21188937 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F5 T1 ZF Inf 2h F5 T1 SAMEA116144996 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F5 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:236 27833 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F5_T1.pair1.truncated ZF_Inf_2h_F5_T1.pair2.truncated fastq fastq 10449733742.0 35250991.0 ena RUN TAB 19 12 2024 10:07:07:236 27834 0:148.22 1:148.22 A:2804774831;C:2419904968;G:2439597584;T:2785285420;N:170939 148 148     2804774831 2419904968 2439597584 2785285420 170939 ERX13488947 ERS21188937 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19157 19157 ERR14086568 ERX13488942 ERS21188932 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F5 T2 ZF Inf 24h F5 T2 SAMEA116144991 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F5 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:231 27823 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F5_T2.pair1.truncated ZF_Inf_24h_F5_T2.pair2.truncated fastq fastq 12646844136.0 42337796.0 ena RUN TAB 19 12 2024 10:07:07:231 27824 0:149.36 1:149.36 A:3482695386;C:2837435668;G:2870976079;T:3455511927;N:225076 149 149     3482695386 2837435668 2870976079 3455511927 225076 ERX13488942 ERS21188932 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19158 19158 ERR14086544 ERX13488918 ERS21188908 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F5 T2 ZF Con 24h F5 T2 SAMEA116144967 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F5 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:204 27775 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F5_T2.pair1.truncated ZF_Con_24h_F5_T2.pair2.truncated fastq fastq 14844040377.0 49765280.0 ena RUN TAB 19 12 2024 10:07:07:204 27776 0:149.14 1:149.14 A:4064105817;C:3361019988;G:3386488696;T:4032154980;N:270896 149 149     4064105817 3361019988 3386488696 4032154980 270896 ERX13488918 ERS21188908 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19159 19159 ERR14086571 ERX13488945 ERS21188935 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F4 T1 ZF Inf 2h F4 T1 SAMEA116144994 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F4 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F4 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:234 27829 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F4_T1.pair1.truncated ZF_Inf_2h_F4_T1.pair2.truncated fastq fastq 12838150223.0 42953821.0 ena RUN TAB 19 12 2024 10:07:07:234 27830 0:149.44 1:149.44 A:3519614186;C:2900824893;G:2922740944;T:3494741243;N:228957 149 149     3519614186 2900824893 2922740944 3494741243 228957 ERX13488945 ERS21188935 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19160 19160 ERR14086549 ERX13488923 ERS21188913 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F5 T1 ZF Con 2h F5 T1 SAMEA116144972 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F5 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:209 27785 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F5_T1.pair1.truncated ZF_Con_2h_F5_T1.pair2.truncated fastq fastq 11835612468.0 39584841.0 ena RUN TAB 19 12 2024 10:07:07:210 27786 0:149.50 1:149.50 A:3269078282;C:2648809055;G:2674404587;T:3243109727;N:210817 149 149     3269078282 2648809055 2674404587 3243109727 210817 ERX13488923 ERS21188913 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19161 19161 ERR14086542 ERX13488916 ERS21188906 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F4 T2 ZF Con 24h F4 T2 SAMEA116144965 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F4 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F4 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:202 27771 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F4_T2.pair1.truncated ZF_Con_24h_F4_T2.pair2.truncated fastq fastq 13798422139.0 46177289.0 ena RUN TAB 19 12 2024 10:07:07:202 27772 0:149.41 1:149.41 A:3775147943;C:3126239757;G:3146905685;T:3749874746;N:254008 149 149     3775147943 3126239757 3146905685 3749874746 254008 ERX13488916 ERS21188906 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19162 19162 ERR14086552 ERX13488926 ERS21188916 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F2 T2 ZF Con 48h F2 T2 SAMEA116144975 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F2 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F2 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:213 27791 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F2_T2.pair1.truncated ZF_Con_48h_F2_T2.pair2.truncated fastq fastq 13264338841.0 44308876.0 ena RUN TAB 19 12 2024 10:07:07:213 27792 0:149.68 1:149.68 A:3659186141;C:2980901976;G:3004156932;T:3619853492;N:240300 149 149     3659186141 2980901976 3004156932 3619853492 240300 ERX13488926 ERS21188916 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19163 19163 ERR14086564 ERX13488938 ERS21188928 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F3 T1 ZF Inf 24h F3 T1 SAMEA116144987 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F3 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:227 27815 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F3_T1.pair1.truncated ZF_Inf_24h_F3_T1.pair2.truncated fastq fastq 10381791769.0 34725644.0 ena RUN TAB 19 12 2024 10:07:07:227 27816 0:149.48 1:149.48 A:2873405143;C:2324734677;G:2341512339;T:2841957730;N:181880 149 149     2873405143 2324734677 2341512339 2841957730 181880 ERX13488938 ERS21188928 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19164 19164 ERR14086578 ERX13488952 ERS21188942 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F3 T2 ZF Inf 48h F3 T2 SAMEA116145001 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F3 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:240 27843 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F3_T2.pair1.truncated ZF_Inf_48h_F3_T2.pair2.truncated fastq fastq 11607933528.0 38797282.0 ena RUN TAB 19 12 2024 10:07:07:241 27844 0:149.60 1:149.60 A:3157510185;C:2647554101;G:2661033132;T:3141630885;N:205225 149 149     3157510185 2647554101 2661033132 3141630885 205225 ERX13488952 ERS21188942 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19165 19165 ERR14086585 ERX13488959 ERS21188949 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F6 T2 ZF Inf 72h F6 T2 SAMEA116145008 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F6 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F6 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:247 27857 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F6_T2.pair1.truncated ZF_Inf_72h_F6_T2.pair2.truncated fastq fastq 14586616716.0 48786392.0 ena RUN TAB 19 12 2024 10:07:07:248 27858 0:149.49 1:149.49 A:4004810052;C:3292146107;G:3307969966;T:3981432519;N:258072 149 149     4004810052 3292146107 3307969966 3981432519 258072 ERX13488959 ERS21188949 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19166 19166 ERR14086569 ERX13488943 ERS21188933 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F3 T1 ZF Inf 2h F3 T1 SAMEA116144992 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F3 T1|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:232 27825 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F3_T1.pair1.truncated ZF_Inf_2h_F3_T1.pair2.truncated fastq fastq 11019441647.0 36982136.0 ena RUN TAB 19 12 2024 10:07:07:232 27826 0:148.98 1:148.98 A:3037955689;C:2470815294;G:2485099673;T:3025375051;N:195940 148 148     3037955689 2470815294 2485099673 3025375051 195940 ERX13488943 ERS21188933 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19167 19167 ERR14086565 ERX13488939 ERS21188929 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F3 T2 ZF Inf 24h F3 T2 SAMEA116144988 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F3 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:228 27817 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F3_T2.pair1.truncated ZF_Inf_24h_F3_T2.pair2.truncated fastq fastq 9871958838.0 32967513.0 ena RUN TAB 19 12 2024 10:07:07:229 27818 0:149.72 1:149.72 A:2712574707;C:2241323417;G:2237990565;T:2680027600;N:42549 149 149     2712574707 2241323417 2237990565 2680027600 42549 ERX13488939 ERS21188929 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19168 19168 ERR14086556 ERX13488930 ERS21188920 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F5 T2 ZF Con 48h F5 T2 SAMEA116144979 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F5 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F5 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:217 27799 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F5_T2.pair1.truncated ZF_Con_48h_F5_T2.pair2.truncated fastq fastq 11861470651.0 39639855.0 ena RUN TAB 19 12 2024 10:07:07:218 27800 0:149.62 1:149.62 A:3258887757;C:2673190405;G:2689128055;T:3240053301;N:211133 149 149     3258887757 2673190405 2689128055 3240053301 211133 ERX13488930 ERS21188920 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19169 19169 ERR14086543 ERX13488917 ERS21188907 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F5 T1 ZF Con 24h F5 T1 SAMEA116144966 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F5 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F5 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:203 27773 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F5_T1.pair1.truncated ZF_Con_24h_F5_T1.pair2.truncated fastq fastq 13831914606.0 46241530.0 ena RUN TAB 19 12 2024 10:07:07:203 27774 0:149.56 1:149.56 A:3799248185;C:3123745954;G:3140306544;T:3768364222;N:249701 149 149     3799248185 3123745954 3140306544 3768364222 249701 ERX13488917 ERS21188907 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19170 19170 ERR14086554 ERX13488928 ERS21188918 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F3 T2 ZF Con 48h F3 T2 SAMEA116144977 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F3 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F3 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:215 27795 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F3_T2.pair1.truncated ZF_Con_48h_F3_T2.pair2.truncated fastq fastq 12448461131.0 41602782.0 ena RUN TAB 19 12 2024 10:07:07:215 27796 0:149.61 1:149.61 A:3389327765;C:2836108569;G:2854509891;T:3368293555;N:221351 149 149     3389327765 2836108569 2854509891 3368293555 221351 ERX13488928 ERS21188918 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19171 19171 ERR14086551 ERX13488925 ERS21188915 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F1 T1 ZF Con 48h F1 T1 SAMEA116144974 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F1 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:211 27789 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F1_T1.pair1.truncated ZF_Con_48h_F1_T1.pair2.truncated fastq fastq 12344084376.0 54459157.0 ena RUN TAB 19 12 2024 10:07:07:212 27790 0:113.33 1:113.33 A:3422797649;C:2748327064;G:2785936911;T:3386774171;N:248581 113 113     3422797649 2748327064 2785936911 3386774171 248581 ERX13488925 ERS21188915 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19172 19172 ERR14086539 ERX13488913 ERS21188903 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F1 T1 ZF Con 24h F1 T1 SAMEA116144962 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F1 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:197 27765 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F1_T1.pair1.truncated ZF_Con_24h_F1_T1.pair2.truncated fastq fastq 10290290855.0 34422082.0 ena RUN TAB 19 12 2024 10:07:07:198 27766 0:149.47 1:149.47 A:2828748546;C:2322992474;G:2336279187;T:2802084735;N:185913 149 149     2828748546 2322992474 2336279187 2802084735 185913 ERX13488913 ERS21188903 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19173 19173 ERR14086563 ERX13488937 ERS21188927 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F2 T2 ZF Inf 24h F2 T2 SAMEA116144986 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F2 T2|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F2 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:226 27813 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F2_T2.pair1.truncated ZF_Inf_24h_F2_T2.pair2.truncated fastq fastq 13536477558.0 45257672.0 ena RUN TAB 19 12 2024 10:07:07:226 27814 0:149.55 1:149.55 A:3725663504;C:3050152384;G:3076823290;T:3683598880;N:239500 149 149     3725663504 3050152384 3076823290 3683598880 239500 ERX13488937 ERS21188927 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19174 19174 ERR14086545 ERX13488919 ERS21188909 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 2h F1 T2 ZF Con 2h F1 T2 SAMEA116144968 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 2h F1 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Con 2h F1 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:205 27777 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_2h_F1_T2.pair1.truncated ZF_Con_2h_F1_T2.pair2.truncated fastq fastq 11201747073.0 37461080.0 ena RUN TAB 19 12 2024 10:07:07:206 27778 0:149.51 1:149.51 A:3081962381;C:2520875203;G:2541328205;T:3057571709;N:9575 149 149     3081962381 2520875203 2541328205 3057571709 9575 ERX13488919 ERS21188909 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19175 19175 ERR14086577 ERX13488951 ERS21188941 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F3 T1 ZF Inf 48h F3 T1 SAMEA116145000 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F3 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F3 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27841 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F3_T1.pair1.truncated ZF_Inf_48h_F3_T1.pair2.truncated fastq fastq 11531780443.0 49868909.0 ena RUN TAB 19 12 2024 10:07:07:240 27842 0:115.62 1:115.62 A:3218054358;C:2544627851;G:2576550932;T:3192371527;N:175775 115 115     3218054358 2544627851 2576550932 3192371527 175775 ERX13488951 ERS21188941 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19176 19176 ERR14086566 ERX13488940 ERS21188930 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F4 T1 ZF Inf 24h F4 T1 SAMEA116144989 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F4 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F4 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:229 27819 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F4_T1.pair1.truncated ZF_Inf_24h_F4_T1.pair2.truncated fastq fastq 11576629501.0 38725250.0 ena RUN TAB 19 12 2024 10:07:07:230 27820 0:149.47 1:149.47 A:3206545757;C:2592097810;G:2606700733;T:3171079624;N:205577 149 149     3206545757 2592097810 2606700733 3171079624 205577 ERX13488940 ERS21188930 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19177 19177 ERR14086582 ERX13488956 ERS21188946 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F5 T1 ZF Inf 72h F5 T1 SAMEA116145005 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F5 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:244 27851 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F5_T1.pair1.truncated ZF_Inf_72h_F5_T1.pair2.truncated fastq fastq 12397801507.0 41450013.0 ena RUN TAB 19 12 2024 10:07:07:245 27852 0:149.55 1:149.55 A:3389701418;C:2810670716;G:2824520271;T:3372689235;N:219867 149 149     3389701418 2810670716 2824520271 3372689235 219867 ERX13488956 ERS21188946 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19178 19178 ERR14086562 ERX13488936 ERS21188926 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F7 T2 ZF Con 72h F7 T2 SAMEA116144985 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F7 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F7 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:225 27811 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F7_T2.pair1.truncated ZF_Con_72h_F7_T2.pair2.truncated fastq fastq 11568689281.0 38694416.0 ena RUN TAB 19 12 2024 10:07:07:225 27812 0:149.49 1:149.49 A:3162387247;C:2620210879;G:2638016970;T:3147868485;N:205700 149 149     3162387247 2620210879 2638016970 3147868485 205700 ERX13488936 ERS21188926 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19179 19179 ERR14086567 ERX13488941 ERS21188931 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 24h F5 T1 ZF Inf 24h F5 T1 SAMEA116144990 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 24h F5 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Inf 24h F5 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:230 27821 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_24h_F5_T1.pair1.truncated ZF_Inf_24h_F5_T1.pair2.truncated fastq fastq 10664451175.0 35656640.0 ena RUN TAB 19 12 2024 10:07:07:231 27822 0:149.54 1:149.54 A:2979287360;C:2367113995;G:2380139534;T:2937759666;N:150620 149 149     2979287360 2367113995 2380139534 2937759666 150620 ERX13488941 ERS21188931 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19180 19180 ERR14086574 ERX13488948 ERS21188938 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F5 T2 ZF Inf 2h F5 T2 SAMEA116144997 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F5 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:237 27835 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F5_T2.pair1.truncated ZF_Inf_2h_F5_T2.pair2.truncated fastq fastq 13456220858.0 45130746.0 ena RUN TAB 19 12 2024 10:07:07:237 27836 0:149.08 1:149.08 A:3757991654;C:2980420740;G:3002285127;T:3715336913;N:186424 149 149     3757991654 2980420740 3002285127 3715336913 186424 ERX13488948 ERS21188938 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19181 19181 ERR14086570 ERX13488944 ERS21188934 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F3 T2 ZF Inf 2h F3 T2 SAMEA116144993 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F3 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F3 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:233 27827 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F3_T2.pair1.truncated ZF_Inf_2h_F3_T2.pair2.truncated fastq fastq 11155932742.0 37312716.0 ena RUN TAB 19 12 2024 10:07:07:233 27828 0:149.49 1:149.49 A:3110035774;C:2469247298;G:2493445096;T:3083048988;N:155586 149 149     3110035774 2469247298 2493445096 3083048988 155586 ERX13488944 ERS21188934 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19182 19182 ERR14086560 ERX13488934 ERS21188924 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F3 T2 ZF Con 72h F3 T2 SAMEA116144983 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F3 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F3 T2|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:222 27807 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F3_T2.pair1.truncated ZF_Con_72h_F3_T2.pair2.truncated fastq fastq 13158999675.0 43988093.0 ena RUN TAB 19 12 2024 10:07:07:223 27808 0:149.57 1:149.57 A:3612242281;C:2968585225;G:2988176368;T:3589814432;N:181369 149 149     3612242281 2968585225 2988176368 3589814432 181369 ERX13488934 ERS21188924 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19183 19183 ERR14086584 ERX13488958 ERS21188948 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F6 T1 ZF Inf 72h F6 T1 SAMEA116145007 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F6 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F6 T1|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:246 27855 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F6_T1.pair1.truncated ZF_Inf_72h_F6_T1.pair2.truncated fastq fastq 11923216836.0 39846317.0 ena RUN TAB 19 12 2024 10:07:07:247 27856 0:149.62 1:149.62 A:3285592694;C:2678630366;G:2695236989;T:3263545610;N:211177 149 149     3285592694 2678630366 2695236989 3263545610 211177 ERX13488958 ERS21188948 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19184 19184 ERR14086575 ERX13488949 ERS21188939 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 48h F1 T2 ZF Inf 48h F1 T2 SAMEA116144998 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 48h F1 T2|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Inf 48h F1 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:238 27837 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_48h_F1_T2.pair1.truncated ZF_Inf_48h_F1_T2.pair2.truncated fastq fastq 11019995708.0 36865197.0 ena RUN TAB 19 12 2024 10:07:07:238 27838 0:149.46 1:149.46 A:3082432761;C:2435008871;G:2450821136;T:3051565998;N:166942 149 149     3082432761 2435008871 2450821136 3051565998 166942 ERX13488949 ERS21188939 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19185 19185 ERR14086558 ERX13488932 ERS21188922 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F2 T1 ZF Con 72h F2 T1 SAMEA116144981 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F2 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:220 27803 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F2_T1.pair1.truncated ZF_Con_72h_F2_T1.pair2.truncated fastq fastq 12158516718.0 40627398.0 ena RUN TAB 19 12 2024 10:07:07:221 27804 0:149.63 1:149.63 A:3326615137;C:2756469221;G:2772700363;T:3302562617;N:169380 149 149     3326615137 2756469221 2772700363 3302562617 169380 ERX13488932 ERS21188922 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19186 19186 ERR14086541 ERX13488915 ERS21188905 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 24h F2 T1 ZF Con 24h F2 T1 SAMEA116144964 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 24h F2 T1|collection date:2021 09 19|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:24|sample name:ZF Con 24h F2 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:201 27769 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_24h_F2_T1.pair1.truncated ZF_Con_24h_F2_T1.pair2.truncated fastq fastq 11404609454.0 38159925.0 ena RUN TAB 19 12 2024 10:07:07:201 27770 0:149.43 1:149.43 A:3146353279;C:2555600785;G:2577318019;T:3125135234;N:202137 149 149     3146353279 2555600785 2577318019 3125135234 202137 ERX13488915 ERS21188905 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19187 19187 ERR14086572 ERX13488946 ERS21188936 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 2h F4 T2 ZF Inf 2h F4 T2 SAMEA116144995 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 2h F4 T2|collection date:2021 09 18|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:2|sample name:ZF Inf 2h F4 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:235 27831 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_2h_F4_T2.pair1.truncated ZF_Inf_2h_F4_T2.pair2.truncated fastq fastq 11812386851.0 39497047.0 ena RUN TAB 19 12 2024 10:07:07:235 27832 0:149.54 1:149.54 A:3313507246;C:2601867632;G:2622018552;T:3274784725;N:208696 149 149     3313507246 2601867632 2622018552 3274784725 208696 ERX13488946 ERS21188936 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19188 19188 ERR14086553 ERX13488927 ERS21188917 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 48h F3 T1 ZF Con 48h F3 T1 SAMEA116144976 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 48h F3 T1|collection date:2021 09 20|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:48|sample name:ZF Con 48h F3 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:214 27793 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_48h_F3_T1.pair1.truncated ZF_Con_48h_F3_T1.pair2.truncated fastq fastq 12860940085.0 43001318.0 ena RUN TAB 19 12 2024 10:07:07:214 27794 0:149.54 1:149.54 A:3516221949;C:2916982714;G:2940303713;T:3487420693;N:11016 149 149     3516221949 2916982714 2940303713 3487420693 11016 ERX13488927 ERS21188917 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19189 19189 ERR14086557 ERX13488931 ERS21188921 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Con 72h F1 T1 ZF Con 72h F1 T1 SAMEA116144980 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Con 72h F1 T1|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Con 72h F1 T1|scientific name:Danio rerio|status:control|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:219 27801 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Con_72h_F1_T1.pair1.truncated ZF_Con_72h_F1_T1.pair2.truncated fastq fastq 12099743905.0 40432008.0 ena RUN TAB 19 12 2024 10:07:07:219 27802 0:149.63 1:149.63 A:3308799221;C:2749018579;G:2763091293;T:3278620227;N:214585 149 149     3308799221 2749018579 2763091293 3278620227 214585 ERX13488931 ERS21188921 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
19190 19190 ERR14086583 ERX13488957 ERS21188947 ERP165174 PRJEB81327 A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis 420c6801-49a8-433c-9e91-52e1fc6cc95a Other Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune r… ENA FIRST PUBLIC:2024 11 01|ENA LAST UPDATE:2024 11 01   ZF Inf 72h F5 T2 ZF Inf 72h F5 T2 SAMEA116145006 CEH,Center for Evolutionary Hologenomics ENA first public:2024 12 19|INSDC center name:CEH Center for Evolutionary Hologenomics|INSDC status:public|Submitter Id:ZF Inf 72h F5 T2|collection date:2021 09 21|common name:zebrafish|geographic location country and/or sea:Denmark|hpi:72|sample name:ZF Inf 72h F5 T2|scientific name:Danio rerio|status:infected|tissue type:gill                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 19 12 2024 10:07:07:245 27853 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP165174 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 ZF_Inf_72h_F5_T2.pair1.truncated ZF_Inf_72h_F5_T2.pair2.truncated fastq fastq 14068176128.0 47037267.0 ena RUN TAB 19 12 2024 10:07:07:246 27854 0:149.54 1:149.54 A:3862187166;C:3174538324;G:3190936465;T:3840265949;N:248224 149 149     3862187166 3174538324 3190936465 3840265949 248224 ERX13488957 ERS21188947 ERA31046805 ceh,center for evolutionary hologenomics|European Nucleotide Archive ceh,center for evolutionary hologenomics                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Denmark 2024-11-01 Undetermined Undetermined Gill Respiratory System
30673 30673 SRR28233239 SRX23844453 SRS20664879 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         A1b01   strain:TRPA1b KO1|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 A1b01 A1b01 A1b01 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     A1b-S1_1.fq.gz A1b-S1_2.fq.gz fastq fastq 10214044500.0 34046815.0 A1b S1 1.fq.gz 0:150 1:150 A:2826731317;C:2254770618;G:2368382524;T:2764027721;N:132320 150 150     2826731317 2254770618 2368382524 2764027721 132320 SRX23844453 SRS20664879 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30674 30674 SRR28233240 SRX23844452 SRS20664878 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT23   strain:WT9|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT23 WT23 WT23 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-2-3_R1.fq.gz WT-2-3_R2.fq.gz fastq fastq 6168655800.0 20562186.0 WT 2 3 R1.fq.gz 0:150 1:150 A:1556231017;C:1526432275;G:1545153210;T:1540414611;N:424687 150 150     1556231017 1526432275 1545153210 1540414611 424687 SRX23844452 SRS20664878 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30675 30675 SRR28233241 SRX23844451 SRS20664877 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT22   strain:WT8|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT22 WT22 WT22 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-2-2_R1.fq.gz WT-2-2_R2.fq.gz fastq fastq 6503274900.0 21677583.0 WT 2 2 R1.fq.gz 0:150 1:150 A:1677274145;C:1574139629;G:1591639511;T:1659773624;N:447991 150 150     1677274145 1574139629 1591639511 1659773624 447991 SRX23844451 SRS20664877 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30676 30676 SRR28233242 SRX23844450 SRS20664876 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT21   strain:WT7|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT21 WT21 WT21 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-2-1_R1.fq.gz WT-2-1_R2.fq.gz fastq fastq 6617487600.0 22058292.0 WT 2 1 R1.fq.gz 0:150 1:150 A:1701231328;C:1606849699;G:1625342674;T:1683607145;N:456754 150 150     1701231328 1606849699 1625342674 1683607145 456754 SRX23844450 SRS20664876 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30677 30677 SRR28233243 SRX23844449 SRS20664875 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT13   strain:WT6|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT13 WT13 WT13 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-1-3_R1.fq.gz WT-1-3_R2.fq.gz fastq fastq 7102153500.0 23673845.0 WT 1 3 R1.fq.gz 0:150 1:150 A:1842496944;C:1707310744;G:1727403195;T:1824440904;N:501713 150 150     1842496944 1707310744 1727403195 1824440904 501713 SRX23844449 SRS20664875 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30678 30678 SRR28233244 SRX23844448 SRS20664874 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT12   strain:WT5|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT12 WT12 WT12 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-1-2_R1.fq.gz WT-1-2_R2.fq.gz fastq fastq 6904290900.0 23014303.0 WT 1 2 R1.fq.gz 0:150 1:150 A:1794495968;C:1655549612;G:1677906470;T:1775860400;N:478450 150 150     1794495968 1655549612 1677906470 1775860400 478450 SRX23844448 SRS20664874 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30679 30679 SRR28233245 SRX23844447 SRS20664873 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT11   strain:WT4|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT11 WT11 WT11 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-1-1_R1.fq.gz WT-1-1_R2.fq.gz fastq fastq 7005297000.0 23350990.0 WT 1 1 R1.fq.gz 0:150 1:150 A:1812285786;C:1684304098;G:1717096826;T:1791123167;N:487123 150 150     1812285786 1684304098 1717096826 1791123167 487123 SRX23844447 SRS20664873 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30680 30680 SRR28233246 SRX23844446 SRS20664872 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         WT03   strain:WT3|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 WT03 WT03 WT03 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     WT-S3_1.fq.gz WT-S3_2.fq.gz fastq fastq 5014921200.0 16716404.0 WT S3 1.fq.gz 0:150 1:150 A:1376105590;C:1123924635;G:1152769107;T:1361994867;N:127001 150 150     1376105590 1123924635 1152769107 1361994867 127001 SRX23844446 SRS20664872 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30681 30681 SRR28233247 SRX23844445 SRS20664871 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         A1b23   strain:TRPA1b KO9|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 A1b23 A1b23 A1b23 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     A1-2-3_R1.fq.gz A1-2-3_R2.fq.gz fastq fastq 6844595700.0 22815319.0 A1 2 3 R1.fq.gz 0:150 1:150 A:1778935800;C:1644607281;G:1662211377;T:1758352025;N:489217 150 150     1778935800 1644607281 1662211377 1758352025 489217 SRX23844445 SRS20664871 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30682 30682 SRR28233248 SRX23844444 SRS20664870 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         A1b22   strain:TRPA1b KO8|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 A1b22 A1b22 A1b22 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     A1-2-2_R1.fq.gz A1-2-2_R2.fq.gz fastq fastq 6529918800.0 21766396.0 A1 2 2 R1.fq.gz 0:150 1:150 A:1681524014;C:1580514490;G:1605344761;T:1662085103;N:450432 150 150     1681524014 1580514490 1605344761 1662085103 450432 SRX23844444 SRS20664870 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30683 30683 SRR28233249 SRX23844443 SRS20664869 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         A1b21   strain:TRPA1b KO7|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 A1b21 A1b21 A1b21 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     A1-2-1_R1.fq.gz A1-2-1_R2.fq.gz fastq fastq 6836499600.0 22788332.0 A1 2 1 R1.fq.gz 0:150 1:150 A:1769098120;C:1648663116;G:1667962343;T:1750293771;N:482250 150 150     1769098120 1648663116 1667962343 1750293771 482250 SRX23844443 SRS20664869 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System
30684 30684 SRR28233250 SRX23844442 SRS20664868 SRP493528 PRJNA1084193 Knockout transcriptome sequencing of TRPA1b gene in zebrafish PRJNA1084193 Other WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment respectively.         A1b13   strain:TRPA1b KO6|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal                 A1b13 A1b13 A1b13 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP493528     A1-1-3_R1.fq.gz A1-1-3_R2.fq.gz fastq fastq 7024153800.0 23413846.0 A1 1 3 R1.fq.gz 0:150 1:150 A:1803658498;C:1704926954;G:1731475860;T:1783603775;N:488713 150 150     1803658498 1704926954 1731475860 1783603775 488713 SRX23844442 SRS20664868 SRA1818205 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-06 Adult Adult Gill Respiratory System

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