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102 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation_coarse = "Respiratory System"

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devstage_curation_coarse 3

devstage_curation 3

tissue_curation_coarse 1

  • Respiratory System · 102 ✖

tissue_curation 1

technology 1

  • unknown · 102 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 102 ✖

experiment.library_layout 1

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
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
38065 38065 SRR1524239 SRX661004 SRS665979 SRP044781 PRJNA255848 Danio rerio Transcriptome PRJNA255848 Transcriptome Analysis Transcriptome analysis of 12 zebrafish tissues parent bioproject:PRJNA255979 pubmed:27189481 Zebrafish gills Zebrafish gills F Dr 3   strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Gills|BioSampleModel:Model organism or animal                 Zebrafish gills F Dr 3 F Dr 3 Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC     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> SRP044781     F_Dr_3_CTTGTA_L002_R1.fastq.gz F_Dr_3_CTTGTA_L002_R2.fastq.gz fastq fastq 10894423200.0 54472116.0 F Dr 3 files 0:100 1:100 A:2975649534;C:2475294028;G:2539728405;T:2894423141;N:9328092 100 100     2975649534 2475294028 2539728405 2894423141 9328092 SRX661004 SRS665979 SRA176464 INRA|Fish Physiology and Genomics INRA PhyloFish 2 0.9252 0.9044 0.11199 0.10966 0.69138 0.69471 0.50738 0.50515 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   France 2015-07-24 Adult Adult Gill Respiratory System
38275 38275 SRR1609740 SRX730393 SRS719614 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   gill10 GSM1523035   source name:gill|tissue:gill|temperature:10°C|strain:Tubingen|age:6 mpf gill10 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... gill fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:gill|temperature:10°C|strain:Tubingen|age:6 mpf GSM1523035 GSM1523035: gill10; Danio rerio; RNA Seq GSM1523035   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523035 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     gill10_2.fq.gz gill10_1.fq.gz fastq fastq 3808228200.0 19041141.0 GSM1523035 r1 0:100 1:100 A:1024211062;C:886771339;G:878140821;T:1019042838;N:62140 100 100     1024211062 886771339 878140821 1019042838 62140 SRX730393 SRS719614 SRA189240 GEO Shanghai Ocean University 2 0.9378 0.93058 0.07663 0.07682 0.73632 0.73894 0.50829 0.50911 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Gill Respiratory System
38276 38276 SRR1609739 SRX730392 SRS719613 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   gill18 GSM1523034   source name:gill|tissue:gill|temperature:18°C|strain:Tubingen|age:6 mpf gill18 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... gill fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:gill|temperature:18°C|strain:Tubingen|age:6 mpf GSM1523034 GSM1523034: gill18; Danio rerio; RNA Seq GSM1523034   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523034 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     gill18_2.fq.gz gill18_1.fq.gz fastq fastq 3364143200.0 16820716.0 GSM1523034 r1 0:100 1:100 A:910167069;C:776115825;G:769784486;T:908021630;N:54190 100 100     910167069 776115825 769784486 908021630 54190 SRX730392 SRS719613 SRA189240 GEO Shanghai Ocean University 2 0.93522 0.92726 0.09078 0.09182 0.69649 0.70041 0.49571 0.5016 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Gill Respiratory System
38277 38277 SRR1609738 SRX730391 SRS719612 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   gill28 GSM1523033   source name:gill|tissue:gill|temperature:28°C|strain:Tubingen|age:6 mpf gill28 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... gill fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:gill|temperature:28°C|strain:Tubingen|age:6 mpf GSM1523033 GSM1523033: gill28; Danio rerio; RNA Seq GSM1523033   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523033 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     gill28_1.fq.gz gill28_2.fq.gz fastq fastq 3195350200.0 15976751.0 GSM1523033 r1 0:100 1:100 A:863344322;C:737593661;G:734637604;T:859709733;N:64880 100 100     863344322 737593661 734637604 859709733 64880 SRX730391 SRS719612 SRA189240 GEO Shanghai Ocean University 2 0.93495 0.93105 0.07061 0.07137 0.70792 0.70999 0.51509 0.52042 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Gill Respiratory System
39705 39705 SRR3579899 SRX1796667 SRS1464820 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 12h gill 3 GSM2176256   source name:gill|tissue:gill|species:zebrafish|replicate:3|time point:12h|temperature:8 degreeC|age:6 mpf zebrafish 8 12h gill 3 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. tissue:gill|species:zebrafish|replicate:3|time point:12h|temperature:8 degreeC|age:6 mpf GSM2176256 GSM2176256: zebrafish 8 12h gill 3; Danio rerio; RNA Seq GSM2176256   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2176256 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     AZ5.R2.fastq.gz AZ5.R1.fastq.gz fastq fastq 3660879450.0 16793025.0 GSM2176256 r1 0:109 1:109 A:976201248;C:849396723;G:852689371;T:979773691;N:2818417 109 109     976201248 849396723 852689371 979773691 2818417 SRX1796667 SRS1464820 SRA273258 GEO Shanghai Ocean University 2 0.93826 0.94162 0.09632 0.09581 0.69292 0.69386 0.46649 0.46447 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2016-05-24 Adult Adult Gill Respiratory System
39706 39706 SRR3579898 SRX1796666 SRS1464819 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 6h gill 3 GSM2176255   source name:gill|tissue:gill|species:zebrafish|replicate:3|time point:6h|temperature:8 degreeC|age:6 mpf zebrafish 8 6h gill 3 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. tissue:gill|species:zebrafish|replicate:3|time point:6h|temperature:8 degreeC|age:6 mpf GSM2176255 GSM2176255: zebrafish 8 6h gill 3; Danio rerio; RNA Seq GSM2176255   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2176255 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     AZ4.R2.fastq.gz AZ4.R1.fastq.gz fastq fastq 3296611478.0 15122071.0 GSM2176255 r1 0:109 1:109 A:878524477;C:766752274;G:767841114;T:880950979;N:2542634 109 109     878524477 766752274 767841114 880950979 2542634 SRX1796666 SRS1464819 SRA273258 GEO Shanghai Ocean University 2 0.94142 0.94349 0.08715 0.08682 0.69073 0.69266 0.50384 0.49966 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2016-05-24 Adult Adult Gill Respiratory System
39707 39707 SRR3579897 SRX1796665 SRS1464818 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 6h gill 2 GSM2176254   source name:gill|tissue:gill|species:zebrafish|replicate:2|time point:6h|temperature:8 degreeC|age:6 mpf zebrafish 8 6h gill 2 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. tissue:gill|species:zebrafish|replicate:2|time point:6h|temperature:8 degreeC|age:6 mpf GSM2176254 GSM2176254: zebrafish 8 6h gill 2; Danio rerio; RNA Seq GSM2176254   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2176254 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     AZ3.R1.fastq.gz AZ3.R2.fastq.gz fastq fastq 3202950394.0 14692433.0 GSM2176254 r1 0:109 1:109 A:857599911;C:740206178;G:741631238;T:861040472;N:2472595 109 109     857599911 740206178 741631238 861040472 2472595 SRX1796665 SRS1464818 SRA273258 GEO Shanghai Ocean University 2 0.92927 0.93296 0.1223 0.12211 0.6801 0.68189 0.49864 0.49957 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2016-05-24 Adult Adult Gill Respiratory System
39708 39708 SRR3579896 SRX1796664 SRS1464817 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 6h gill 1 GSM2176253   source name:gill|tissue:gill|species:zebrafish|replicate:1|time point:6h|temperature:8 degreeC|age:6 mpf zebrafish 8 6h gill 1 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. tissue:gill|species:zebrafish|replicate:1|time point:6h|temperature:8 degreeC|age:6 mpf GSM2176253 GSM2176253: zebrafish 8 6h gill 1; Danio rerio; RNA Seq GSM2176253   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2176253 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     AZ2.R1.fastq.gz AZ2.R2.fastq.gz fastq fastq 3207505722.0 14713329.0 GSM2176253 r1 0:109 1:109 A:855447431;C:743239876;G:742942682;T:863378143;N:2497590 109 109     855447431 743239876 742942682 863378143 2497590 SRX1796664 SRS1464817 SRA273258 GEO Shanghai Ocean University 2 0.93016 0.93443 0.11754 0.11651 0.69023 0.69213 0.50033 0.5004 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2016-05-24 Adult Adult Gill Respiratory System
39709 39709 SRR3579895 SRX1796663 SRS1464816 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 0h gill 3 GSM2176252   source name:gill|tissue:gill|species:zebrafish|replicate:3|time point:0h|temperature:8 degreeC|age:6 mpf zebrafish 8 0h gill 3 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. tissue:gill|species:zebrafish|replicate:3|time point:0h|temperature:8 degreeC|age:6 mpf GSM2176252 GSM2176252: zebrafish 8 0h gill 3; Danio rerio; RNA Seq GSM2176252   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2176252 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     AZ1.R1.fastq.gz AZ1.R2.fastq.gz fastq fastq 2657966090.0 12192505.0 GSM2176252 r1 0:109 1:109 A:707609624;C:618473475;G:616075644;T:713757642;N:2049705 109 109     707609624 618473475 616075644 713757642 2049705 SRX1796663 SRS1464816 SRA273258 GEO Shanghai Ocean University 2 0.93562 0.9391 0.0969 0.09613 0.68124 0.68288 0.49352 0.48196 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2016-05-24 Adult Adult Gill Respiratory System
39710 39710 SRR2067888 SRX1063367 SRS963393 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 12h gill 2 GSM1714084   source name:gill|age:6 months|tissue:gill|group:11|replicate:2|condition:LOE 12h|temperature:8°C zebrafish 8 12h gill 2 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:11|replicate:2|condition:LOE 12h|temperature:8°C GSM1714084 GSM1714084: zebrafish 8 12h gill 2; Danio rerio; RNA Seq GSM1714084   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714084 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_LOE_12h_gill_2_2.fq.gz zebrafish_LOE_12h_gill_2_1.fq.gz fastq fastq 3433893272.0 15751804.0 GSM1714084 r1 0:109 1:109 A:929285053;C:798076747;G:794515113;T:911786961;N:229398 109 109     929285053 798076747 794515113 911786961 229398 SRX1063367 SRS963393 SRA273258 GEO Shanghai Ocean University 2 0.89177 0.89023 0.11452 0.11377 0.69684 0.69917 0.4984 0.50064 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
39711 39711 SRR2067887 SRX1063366 SRS963395 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 12h gill 1 GSM1714083   source name:gill|age:6 months|tissue:gill|group:11|replicate:1|condition:LOE 12h|temperature:8°C zebrafish 8 12h gill 1 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:11|replicate:1|condition:LOE 12h|temperature:8°C GSM1714083 GSM1714083: zebrafish 8 12h gill 1; Danio rerio; RNA Seq GSM1714083   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714083 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_LOE_12h_gill_1_1.fq.gz zebrafish_LOE_12h_gill_1_2.fq.gz fastq fastq 2809269426.0 12886557.0 GSM1714083 r1 0:109 1:109 A:746647853;C:662133538;G:660978954;T:739327059;N:182022 109 109     746647853 662133538 660978954 739327059 182022 SRX1063366 SRS963395 SRA273258 GEO Shanghai Ocean University 2 0.90881 0.90909 0.10589 0.10574 0.69307 0.69552 0.49893 0.4996 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
39712 39712 SRR2067886 SRX1063365 SRS963394 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 0h gill 2 GSM1714082   source name:gill|age:6 months|tissue:gill|group:10|replicate:2|condition:LOE 0h|temperature:8°C zebrafish 8 0h gill 2 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:10|replicate:2|condition:LOE 0h|temperature:8°C GSM1714082 GSM1714082: zebrafish 8 0h gill 2; Danio rerio; RNA Seq GSM1714082   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714082 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_LOE_0h_gill_2_2.fq.gz zebrafish_LOE_0h_gill_2_1.fq.gz fastq fastq 3314206040.0 15202780.0 GSM1714082 r1 0:109 1:109 A:876309775;C:785596042;G:783767015;T:868315301;N:217907 109 109     876309775 785596042 783767015 868315301 217907 SRX1063365 SRS963394 SRA273258 GEO Shanghai Ocean University 2 0.91374 0.91359 0.10013 0.1009 0.69112 0.69353 0.49181 0.49578 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
39713 39713 SRR2067884 SRX1063364 SRS963397 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 8 0h gill 1 GSM1714081   source name:gill|age:6 months|tissue:gill|group:10|replicate:1|condition:LOE 0h|temperature:8°C zebrafish 8 0h gill 1 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:10|replicate:1|condition:LOE 0h|temperature:8°C GSM1714081 GSM1714081: zebrafish 8 0h gill 1; Danio rerio; RNA Seq GSM1714081   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714081 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_LOE_0h_gill_1_2.fq.gz zebrafish_LOE_0h_gill_1_1.fq.gz fastq fastq 3365277336.0 15437052.0 GSM1714081 r1 0:109 1:109 A:886390709;C:799926200;G:799651565;T:879089225;N:219637 109 109     886390709 799926200 799651565 879089225 219637 SRX1063364 SRS963397 SRA273258 GEO Shanghai Ocean University 2 0.91394 0.91483 0.09867 0.09893 0.68641 0.68968 0.49615 0.49076 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
39714 39714 SRR2067883 SRX1063363 SRS963396 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 28 gill 3 GSM1714080   source name:gill|age:6 months|tissue:gill|group:9|replicate:3|condition:28°C|temperature:28°C zebrafish 28 gill 3 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:9|replicate:3|condition:28°C|temperature:28°C GSM1714080 GSM1714080: zebrafish 28 gill 3; Danio rerio; RNA Seq GSM1714080   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714080 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_28_gill_3_1.fq.gz zebrafish_28_gill_3_2.fq.gz fastq fastq 3254092540.0 14927030.0 GSM1714080 r1 0:109 1:109 A:858267547;C:771084069;G:771064626;T:853459447;N:216851 109 109     858267547 771084069 771064626 853459447 216851 SRX1063363 SRS963396 SRA273258 GEO Shanghai Ocean University 2 0.90316 0.90236 0.08907 0.08895 0.67823 0.6802 0.49089 0.49051 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
39715 39715 SRR2067882 SRX1063362 SRS963398 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 28 gill 2 GSM1714079   source name:gill|age:6 months|tissue:gill|group:9|replicate:2|condition:28°C|temperature:28°C zebrafish 28 gill 2 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:9|replicate:2|condition:28°C|temperature:28°C GSM1714079 GSM1714079: zebrafish 28 gill 2; Danio rerio; RNA Seq GSM1714079   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714079 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_28_gill_2_2.fq.gz zebrafish_28_gill_2_1.fq.gz fastq fastq 2621117986.0 12023477.0 GSM1714079 r1 0:109 1:109 A:690118661;C:623432564;G:622600619;T:684797673;N:168469 109 109     690118661 623432564 622600619 684797673 168469 SRX1063362 SRS963398 SRA273258 GEO Shanghai Ocean University 2 0.90329 0.90413 0.08957 0.09004 0.67529 0.67673 0.49233 0.49384 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
39716 39716 SRR2067881 SRX1063361 SRS963399 SRP059605 PRJNA287283 Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish GSE69965 Other Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL namely the lower end of survival temperature is an important trait delimiting the geographical distribution of a species however the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus which were reared at a common temperature 28°C but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia 8°C. Five KEGG pathways were found sequentially over represented in the zebrafish/tilapia divergently expressed genes in the duration 12 hour of 8°C exposure forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.  Overall design: Examination of gene expressional divergence in gill between zebrafish and tilapia   pubmed:27356472   zebrafish 28 gill 1 GSM1714078   source name:gill|age:6 months|tissue:gill|group:9|replicate:1|condition:28°C|temperature:28°C zebrafish 28 gill 1 Illumina Casava1.7 software used for basecalling. Trimmomatic 0.32 was used to remove the adaptor sequence and low quality bases from the raw reads. First the parameter in ILLUMINACLIP was set to 2:30:10 to remove the adaptor sequences from the raw reads. Then the 2 bases from the start and the end of the read were removed. A sliding window trimming was conducted to cut the reads when the average quality within 4 bases falls below 20 and post trimming length of 50 bases or longer are enforced. Finally the trimmed reads that were paired were kept for the mapping. Tophat 2.0.13 was used to map the reads to the reference genomes. Samtools was used to first sort the bam files of the aligned reads by the read name. HTSeq count was then applied to count the number of reads that are mapped to the genes. Genome build: tilapia and zebrafish genome sequence and gtf files were downloaded from the Ensembl release 78 Supplementary files format and content: tab delimited text files include raw reads count for each Sample gill Fishes were subjected to a stepped cooling by lowering 1°C /h to 8°C and then maintained at 8°C. When temperature declined to 8°C tialpia loss of equilibrium which was denoted 0h of LOE in this study. At 28°C 0h of LOE 6h of LOE and 12h of LOE gill and/or kidney from both fish species were collected and approximately same amount of each tissue were pooled. In addition post 6h of LOE tilapia was transferred to recovery tank and hold for 6h. Tissues from the recovery tilapia were collected for RNA seq. Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols Tilapia and zebrafish were raised and maintained at 28±1°C in well managed aquariums. age:6 months|tissue:gill|group:9|replicate:1|condition:28°C|temperature:28°C GSM1714078 GSM1714078: zebrafish 28 gill 1; Danio rerio; RNA Seq GSM1714078   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1714078 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP059605     zebrafish_28_gill_1_1.fq.gz zebrafish_28_gill_1_2.fq.gz fastq fastq 2867801336.0 13155052.0 GSM1714078 r1 0:109 1:109 A:765671592;C:675469841;G:688613306;T:737863609;N:182988 109 109     765671592 675469841 688613306 737863609 182988 SRX1063361 SRS963399 SRA273258 GEO Shanghai Ocean University 2 0.90743 0.9075 0.08734 0.08732 0.68158 0.68199 0.48076 0.4913 109 109 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2015-06-17 Adult Adult Gill Respiratory System
61563 61563 SRR12876831 SRX9342872 SRS7564561 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 1 gill GA101   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 10 days rep 1|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA101 GA101 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA101_1.fq.gz GA101_2.fq.gz fastq fastq 6611109300.0 22037031.0 GA101 1.fq.gz 0:150 1:150 A:1822314146;C:1471850683;G:1510322104;T:1806538309;N:84058 150 150     1822314146 1471850683 1510322104 1806538309 84058 SRX9342872 SRS7564561 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.88995 0.88981 0.12485 0.12443 0.68789 0.68984 0.48666 0.48975 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61564 61564 SRR12876832 SRX9342871 SRS7564560 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 3 gill GA53   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 5 days rep 3|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA53 GA53 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA53_1.fq.gz GA53_2.fq.gz fastq fastq 8283385800.0 27611286.0 GA53 1.fq.gz 0:150 1:150 A:2239826150;C:1885634833;G:1947119012;T:2210697737;N:108068 150 150     2239826150 1885634833 1947119012 2210697737 108068 SRX9342871 SRS7564560 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.90114 0.89712 0.10906 0.10849 0.69333 0.69623 0.49705 0.49611 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61565 61565 SRR12876833 SRX9342870 SRS7564559 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 2 gill GA52   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 5 days rep 2|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA52 GA52 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA52_1.fq.gz GA52_2.fq.gz fastq fastq 8670404400.0 28901348.0 GA52 1.fq.gz 0:150 1:150 A:2374606477;C:1944386214;G:2008885037;T:2342413945;N:112727 150 150     2374606477 1944386214 2008885037 2342413945 112727 SRX9342870 SRS7564559 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89583 0.89534 0.11185 0.11148 0.68949 0.69404 0.50005 0.4999 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61566 61566 SRR12876834 SRX9342869 SRS7564557 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 1 gill GA51   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 5 days rep 1|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA51 GA51 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA51_1.fq.gz GA51_2.fq.gz fastq fastq 8691274800.0 28970916.0 GA51 1.fq.gz 0:150 1:150 A:2342548372;C:1990456213;G:2049330462;T:2308826988;N:112765 150 150     2342548372 1990456213 2049330462 2308826988 112765 SRX9342869 SRS7564557 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.91033 0.906 0.08972 0.08899 0.6957 0.69861 0.49987 0.50148 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61567 61567 SRR12876835 SRX9342868 SRS7564558 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 3 gill GA13   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 1 days rep 3|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA13 GA13 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA13_1.fq.gz GA13_2.fq.gz fastq fastq 7710021900.0 25700073.0 GA13 1.fq.gz 0:150 1:150 A:2125488812;C:1725849787;G:1761464256;T:2097118672;N:100373 150 150     2125488812 1725849787 1761464256 2097118672 100373 SRX9342868 SRS7564558 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.88792 0.88661 0.12113 0.12183 0.68353 0.68542 0.48427 0.47881 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61568 61568 SRR12876836 SRX9342867 SRS7564556 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 2 gill GA12   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 1 days rep 2|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA12 GA12 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA12_1.fq.gz GA12_2.fq.gz fastq fastq 9047943300.0 30159811.0 GA12 1.fq.gz 0:150 1:150 A:2446256124;C:2072854635;G:2118183379;T:2410532088;N:117074 150 150     2446256124 2072854635 2118183379 2410532088 117074 SRX9342867 SRS7564556 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.91262 0.90813 0.09206 0.09161 0.69438 0.69601 0.50411 0.49221 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61569 61569 SRR12876837 SRX9342866 SRS7564554 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 1 gill GA11   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 1 days rep 1|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA11 GA11 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA11_1.fq.gz GA11_2.fq.gz fastq fastq 8188340700.0 27294469.0 GA11 1.fq.gz 0:150 1:150 A:2244984253;C:1843643944;G:1885403234;T:2214203077;N:106192 150 150     2244984253 1843643944 1885403234 2214203077 106192 SRX9342866 SRS7564554 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.8921 0.89037 0.11594 0.11574 0.69008 0.69175 0.49696 0.49028 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61570 61570 SRR12876838 SRX9342865 SRS7564555 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 3 control group GCK3   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:control 3 rep 3|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GCK3 GCK3 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GCK3_1.fq.gz GCK3_2.fq.gz fastq fastq 8496632100.0 28322107.0 GCK3 1.fq.gz 0:150 1:150 A:2320649109;C:1922298481;G:1966289269;T:2287285557;N:109684 150 150     2320649109 1922298481 1966289269 2287285557 109684 SRX9342865 SRS7564555 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.90465 0.89673 0.09949 0.09852 0.69729 0.69982 0.502 0.50819 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61571 61571 SRR12876839 SRX9342864 SRS7564553 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 3 gill GC53   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:300 μm MPs 5 days rep 3|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GC53 GC53 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GC53_1.fq.gz GC53_2.fq.gz fastq fastq 7791811800.0 25972706.0 GC53 1.fq.gz 0:150 1:150 A:2114921024;C:1768926177;G:1805603416;T:2102260456;N:100727 150 150     2114921024 1768926177 1805603416 2102260456 100727 SRX9342864 SRS7564553 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89598 0.89109 0.09576 0.09456 0.69096 0.69229 0.48722 0.48535 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61572 61572 SRR12876840 SRX9342863 SRS7564552 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 2 gill GC52   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:300 μm MPs 5 days rep 2|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GC52 GC52 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GC52_1.fq.gz GC52_2.fq.gz fastq fastq 7659995100.0 25533317.0 GC52 1.fq.gz 0:150 1:150 A:2095841598;C:1728049655;G:1751039123;T:2084966530;N:98194 150 150     2095841598 1728049655 1751039123 2084966530 98194 SRX9342863 SRS7564552 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89551 0.89201 0.12025 0.11984 0.68704 0.6887 0.49253 0.49124 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61573 61573 SRR12876841 SRX9342862 SRS7564551 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 1 gill GC51   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:300 μm MPs 5 days rep 1|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GC51 GC51 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GC51_1.fq.gz GC51_2.fq.gz fastq fastq 8250604500.0 27502015.0 GC51 1.fq.gz 0:150 1:150 A:2277658526;C:1841180318;G:1864740304;T:2266914596;N:110756 150 150     2277658526 1841180318 1864740304 2266914596 110756 SRX9342862 SRS7564551 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89007 0.88613 0.12691 0.12602 0.68392 0.68682 0.49649 0.48768 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61574 61574 SRR12876842 SRX9342861 SRS7564549 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 3 gill GB53   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:100 μm MPs 5 days rep 3|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GB53 GB53 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GB53_1.fq.gz GB53_2.fq.gz fastq fastq 7746441900.0 25821473.0 GB53 1.fq.gz 0:150 1:150 A:2115754935;C:1752015286;G:1790064440;T:2088504916;N:102323 150 150     2115754935 1752015286 1790064440 2088504916 102323 SRX9342861 SRS7564549 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89804 0.89215 0.10792 0.10708 0.6883 0.69142 0.50315 0.50276 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61575 61575 SRR12876843 SRX9342860 SRS7564550 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 2 gill GB52   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:100 μm MPs 5 days rep 2|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GB52 GB52 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GB52_1.fq.gz GB52_2.fq.gz fastq fastq 6475149900.0 21583833.0 GB52 1.fq.gz 0:150 1:150 A:1774993184;C:1454719205;G:1483806999;T:1761543638;N:86874 150 150     1774993184 1454719205 1483806999 1761543638 86874 SRX9342860 SRS7564550 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89141 0.89034 0.13121 0.13087 0.68899 0.69039 0.4891 0.48326 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61576 61576 SRR12876844 SRX9342859 SRS7564548 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 1 gill GB51   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:100 μm MPs 5 days rep 1|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GB51 GB51 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GB51_1.fq.gz GB51_2.fq.gz fastq fastq 6779179500.0 22597265.0 GB51 1.fq.gz 0:150 1:150 A:1843230337;C:1532685650;G:1586324656;T:1816850451;N:88406 150 150     1843230337 1532685650 1586324656 1816850451 88406 SRX9342859 SRS7564548 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.89894 0.8979 0.1116 0.1104 0.69426 0.69698 0.49254 0.48734 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61577 61577 SRR12876845 SRX9342858 SRS7564547 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 3 gill GA103   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 10 days rep 3|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA103 GA103 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA103_1.fq.gz GA103_2.fq.gz fastq fastq 5852867100.0 19509557.0 GA103 1.fq.gz 0:150 1:150 A:1613843518;C:1306034750;G:1328364824;T:1604547905;N:76103 150 150     1613843518 1306034750 1328364824 1604547905 76103 SRX9342858 SRS7564547 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.88762 0.88673 0.13145 0.13183 0.68692 0.68858 0.50044 0.50102 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 Adult Adult Gill Respiratory System
61578 61578 SRR12876846 SRX9342857 SRS7564546 SRP288136 PRJNA670521 Transcriptome sequencing of zebrafish Danio rerio gill tissue PRJNA670521 Other Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     replicate 2 gill GA102   isolate:missing|breed:zebrafish|age:more than 4 month|dev stage:adult|sex:pooled male and female|tissue:gill|treatment:50 μm MPs 10 days rep 2|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish Danio rerio gill tissue GA102 GA102 Transcriptome sequencing of zebrafish Danio rerio gill tissue in response to microplastics     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP288136     GA102_1.fq.gz GA102_2.fq.gz fastq fastq 6012503700.0 20041679.0 GA102 1.fq.gz 0:150 1:150 A:1669287123;C:1330267050;G:1355857820;T:1657010667;N:81040 150 150     1669287123 1330267050 1355857820 1657010667 81040 SRX9342857 SRS7564546 SRA1146301 Ministry of Agriculture and Rural Affairs|Rural Energy and Environment Agency Ministry of Agriculture and Rural Affairs 2 0.88739 0.88671 0.13257 0.13166 0.68649 0.68876 0.49895 0.49244 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2020-10-22 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");;