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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
9842,ERR4029259,ERX4030575,ERS4514128,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 4,SAMEA6786449,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786449|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 4 p,Sample 4 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S41_R1_001.fastq.gz FB4_S41_R2_001.fastq.gz,fastq fastq,4354809436.0,29071030.0,E MTAB 8958:FB4 S41 R,0:74.90 1:74.90,A:1140431810;C:1005396495;G:1008528915;T:1171220102;N:29232114,74,74,,,1140431810,1005396495,1008528915,1171220102,29232114,ERX4030575,ERS4514128,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91143,0.91076,0.10123,0.09941,0.68235,0.68452,0.48713,0.48998,76,74,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9843,ERR4029258,ERX4030574,ERS4514127,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 3,SAMEA6786448,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786448|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 3 p,Sample 3 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S40_R1_001.fastq.gz FB3_S40_R2_001.fastq.gz,fastq fastq,3973860397.0,26559713.0,E MTAB 8958:FB3 S40 R,0:74.80 1:74.82,A:1038749031;C:917944667;G:920080717;T:1066160216;N:30925766,74,74,,,1038749031,917944667,920080717,1066160216,30925766,ERX4030574,ERS4514127,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91065,0.90981,0.10133,0.09911,0.68789,0.68945,0.47182,0.49996,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9844,ERR4029257,ERX4030573,ERS4514126,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 2,SAMEA6786447,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786447|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 2 p,Sample 2 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S39_R1_001.fastq.gz FB2_S39_R2_001.fastq.gz,fastq fastq,4135184845.0,27517010.0,E MTAB 8958:FB2 S39 R,0:75.15 1:75.13,A:1084253902;C:962303819;G:961163738;T:1111949967;N:15513419,75,75,,,1084253902,962303819,961163738,1111949967,15513419,ERX4030573,ERS4514126,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91098,0.91057,0.09468,0.09311,0.68095,0.68282,0.49982,0.50146,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9845,ERR4029256,ERX4030572,ERS4514125,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 1,SAMEA6786446,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786446|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 1 p,Sample 1 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 06 17,FB1_S38_R1_001.fastq FB1_S38_R2_001.fastq,fastq fastq,4651073045.0,31021879.0,E MTAB 8958:FB1 S38 R,0:74.96 1:74.97,A:1225305023;C:1072643957;G:1069905162;T:1255950159;N:27268744,74,74,,,1225305023,1072643957,1069905162,1255950159,27268744,ERX4030572,ERS4514125,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91441,0.91282,0.10095,0.09913,0.686,0.68745,0.49433,0.5047,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9846,ERR4029255,ERX4030571,ERS4514124,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 16,SAMEA6786445,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786445|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 16|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 16|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 16 p,Sample 16 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S20_R1_001.fastq.gz FB4_S20_R2_001.fastq.gz,fastq fastq,5961540086.0,39717871.0,E MTAB 8958:FB4 S20 R,0:75.07 1:75.03,A:1565483441;C:1390303898;G:1372759826;T:1611361282;N:21631639,75,75,,,1565483441,1390303898,1372759826,1611361282,21631639,ERX4030571,ERS4514124,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90959,0.90989,0.0925,0.09172,0.68787,0.68929,0.49093,0.49057,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9847,ERR4029254,ERX4030570,ERS4514123,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 15,SAMEA6786444,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786444|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 15|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 15|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 15 p,Sample 15 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S19_R1_001.fastq.gz FB3_S19_R2_001.fastq.gz,fastq fastq,6835575760.0,45515064.0,E MTAB 8958:FB3 S19 R,0:75.11 1:75.07,A:1802176562;C:1589590146;G:1564279107;T:1858606235;N:20923710,75,75,,,1802176562,1589590146,1564279107,1858606235,20923710,ERX4030570,ERS4514123,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90945,0.91123,0.09519,0.09378,0.67963,0.67961,0.49246,0.49476,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9848,ERR4029253,ERX4030569,ERS4514122,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 14,SAMEA6786443,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786443|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 14|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 14|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 14 p,Sample 14 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S18_R1_001.fastq.gz FB2_S18_R2_001.fastq.gz,fastq fastq,5789923311.0,38517674.0,E MTAB 8958:FB2 S18 R,0:75.18 1:75.14,A:1520250885;C:1354960735;G:1336204150;T:1565011084;N:13496457,75,75,,,1520250885,1354960735,1336204150,1565011084,13496457,ERX4030569,ERS4514122,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91863,0.91917,0.08923,0.08753,0.68848,0.68883,0.5042,0.50799,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9849,ERR4029252,ERX4030568,ERS4514121,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 13,SAMEA6786442,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786442|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 13|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 13|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 13 p,Sample 13 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB1_S17_R1_001.fastq.gz FB1_S17_R2_001.fastq.gz,fastq fastq,6951804793.0,46295025.0,E MTAB 8958:FB1 S17 R,0:75.10 1:75.06,A:1827618209;C:1618955946;G:1595802123;T:1884739421;N:24689094,75,75,,,1827618209,1618955946,1595802123,1884739421,24689094,ERX4030568,ERS4514121,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90991,0.90972,0.09297,0.09193,0.68284,0.68392,0.49878,0.5017,74,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9850,ERR4029251,ERX4030567,ERS4514120,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 20,SAMEA6786441,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786441|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 20|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / ; il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 20|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 20 p,Sample 20 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a   / ; il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB4_S44_R1_001.fastq.gz FB4_S44_R2_001.fastq.gz,fastq fastq,9629684100.0,64667395.0,E MTAB 8958:FB4 S44 R,0:74.47 1:74.44,A:2552333346;C:2176006333;G:2180111416;T:2614191329;N:107041676,74,74,,,2552333346,2176006333,2180111416,2614191329,107041676,ERX4030567,ERS4514120,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90795,0.90756,0.10044,0.09789,0.6888,0.69256,0.50043,0.4932,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9851,ERR4029250,ERX4030566,ERS4514119,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 19,SAMEA6786440,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786440|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 19|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / ; il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 19|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 19 p,Sample 19 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a   / ; il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB3_S43_R1_001.fastq.gz FB3_S43_R2_001.fastq.gz,fastq fastq,11268744444.0,75088756.0,E MTAB 8958:FB3 S43 R,0:75.06 1:75.01,A:2983863814;C:2608268633;G:2555098938;T:3072413168;N:49099891,75,75,,,2983863814,2608268633,2555098938,3072413168,49099891,ERX4030566,ERS4514119,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9107,0.91089,0.09522,0.09428,0.69187,0.69266,0.49302,0.49463,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9852,ERR4029249,ERX4030565,ERS4514118,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 18,SAMEA6786439,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786439|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 18|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / ; il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 18|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 18 p,Sample 18 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a   / ; il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB2_S42_R1_001.fastq.gz FB2_S42_R2_001.fastq.gz,fastq fastq,10434072067.0,69530304.0,E MTAB 8958:FB2 S42 R,0:75.06 1:75.01,A:2749500618;C:2426208950;G:2375421255;T:2834879202;N:48062042,75,75,,,2749500618,2426208950,2375421255,2834879202,48062042,ERX4030565,ERS4514118,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9084,0.90779,0.0926,0.0917,0.68809,0.68864,0.49817,0.49902,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9853,ERR4029248,ERX4030564,ERS4514117,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 17,SAMEA6786438,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786438|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 17|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / ; il4/13b  / |organism part:gill|sample name:E MTAB 8958:Sample 17|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 17 p,Sample 17 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a   / ; il4/13b  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB1_S41_R1_001.fastq.gz FB1_S41_R2_001.fastq.gz,fastq fastq,12125040750.0,80781224.0,E MTAB 8958:FB1 S41 R,0:75.08 1:75.02,A:3129480022;C:2890038396;G:2819859086;T:3233228646;N:52434600,75,75,,,3129480022,2890038396,2819859086,3233228646,52434600,ERX4030564,ERS4514117,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91384,0.91301,0.10967,0.10615,0.69006,0.69041,0.51643,0.51985,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9854,ERR4029247,ERX4030563,ERS4514116,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 8,SAMEA6786437,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786437|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / |organism part:gill|sample name:E MTAB 8958:Sample 8|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 8 p,Sample 8 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB12_S49_R1_001.fastq.gz FB12_S49_R2_001.fastq.gz,fastq fastq,4223131851.0,28165494.0,E MTAB 8958:FB12 S49 R,0:74.95 1:74.99,A:1121514270;C:962554300;G:967294488;T:1146544647;N:25224146,74,74,,,1121514270,962554300,967294488,1146544647,25224146,ERX4030563,ERS4514116,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91639,0.91413,0.10604,0.10326,0.68162,0.68458,0.49921,0.50172,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9855,ERR4029246,ERX4030562,ERS4514115,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 7,SAMEA6786436,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786436|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / |organism part:gill|sample name:E MTAB 8958:Sample 7|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 7 p,Sample 7 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB11_S48_R1_001.fastq.gz FB11_S48_R2_001.fastq.gz,fastq fastq,4670407305.0,31054128.0,E MTAB 8958:FB11 S48 R,0:75.20 1:75.19,A:1234494738;C:1078360233;G:1084251975;T:1258088405;N:15211954,75,75,,,1234494738,1078360233,1084251975,1258088405,15211954,ERX4030562,ERS4514115,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.92228,0.92038,0.09418,0.09222,0.68674,0.68862,0.48948,0.48842,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9856,ERR4029245,ERX4030561,ERS4514114,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 6,SAMEA6786435,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786435|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / |organism part:gill|sample name:E MTAB 8958:Sample 6|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 6 p,Sample 6 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB10_S47_R1_001.fastq.gz FB10_S47_R2_001.fastq.gz,fastq fastq,3970723047.0,26597167.0,E MTAB 8958:FB10 S47 R,0:74.63 1:74.66,A:1037861230;C:915437247;G:922979694;T:1056625196;N:37819680,74,74,,,1037861230,915437247,922979694,1056625196,37819680,ERX4030561,ERS4514114,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.92474,0.92246,0.0934,0.0916,0.69106,0.69384,0.49058,0.48154,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9857,ERR4029244,ERX4030560,ERS4514113,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 5,SAMEA6786434,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786434|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a  / |organism part:gill|sample name:E MTAB 8958:Sample 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 5 p,Sample 5 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il4/13a  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB9_S46_R1_001.fastq.gz FB9_S46_R2_001.fastq.gz,fastq fastq,4267946165.0,28455064.0,E MTAB 8958:FB9 S46 R,0:75.00 1:74.99,A:1108310330;C:999732020;G:987857724;T:1148193980;N:23852111,75,74,,,1108310330,999732020,987857724,1148193980,23852111,ERX4030560,ERS4514113,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.9223,0.91737,0.09304,0.09006,0.69063,0.6929,0.48978,0.49675,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9858,ERR4029243,ERX4030559,ERS4514112,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 9,SAMEA6786433,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786433|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10  / |organism part:gill|sample name:E MTAB 8958:Sample 9|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 9 p,Sample 9 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB17_S54_R1_001.fastq.gz FB17_S54_R2_001.fastq.gz,fastq fastq,3847723303.0,25764874.0,E MTAB 8958:FB17 S54 R,0:74.65 1:74.69,A:1009950686;C:883047473;G:885821368;T:1035313325;N:33590451,74,74,,,1009950686,883047473,885821368,1035313325,33590451,ERX4030559,ERS4514112,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91088,0.90785,0.09899,0.09623,0.68822,0.69055,0.48686,0.49337,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9859,ERR4029242,ERX4030558,ERS4514111,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 12,SAMEA6786432,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786432|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10  / |organism part:gill|sample name:E MTAB 8958:Sample 12|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 12 p,Sample 12 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB20_S57_R1_001.fastq.gz FB20_S57_R2_001.fastq.gz,fastq fastq,4534822065.0,30209756.0,E MTAB 8958:FB20 S57 R,0:75.06 1:75.06,A:1181838544;C:1056097162;G:1066594521;T:1207484216;N:22807622,75,75,,,1181838544,1056097162,1066594521,1207484216,22807622,ERX4030558,ERS4514111,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91577,0.91513,0.09598,0.09473,0.68931,0.69132,0.49181,0.49786,74,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9860,ERR4029241,ERX4030557,ERS4514110,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 11,SAMEA6786431,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786431|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 11|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10  / |organism part:gill|sample name:E MTAB 8958:Sample 11|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 11 p,Sample 11 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB19_S56_R1_001.fastq.gz FB19_S56_R2_001.fastq.gz,fastq fastq,5070571422.0,33987501.0,E MTAB 8958:FB19 S56 R,0:74.58 1:74.61,A:1327496786;C:1163563377;G:1162870630;T:1365191685;N:51448944,74,74,,,1327496786,1163563377,1162870630,1365191685,51448944,ERX4030557,ERS4514110,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.91091,0.91003,0.09944,0.09748,0.68745,0.69016,0.49706,0.49287,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
9861,ERR4029240,ERX4030556,ERS4514109,ERP121190,PRJEB37851,Zebrafish il 4 il 10 regulated immunity in gills,E-MTAB-8958,Transcriptome Analysis,The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However  how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here  we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint  we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals  zebrafish il10 appears to have an anti inflammatory function.,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,,Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end.,Sample 10,SAMEA6786430,UNIVERSITY OF MANCHESTER,ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786430|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10  / |organism part:gill|sample name:E MTAB 8958:Sample 10|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,E MTAB 8958:Sample 10 p,Sample 10 p,Zebrafish il 4 il 10 regulated immunity in gills,This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype  il4/13a KO  il4/13b KO  il4/13a;b KO and il10 KO. The strains il4/13a KO  il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the  il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW  Busch nentwich EM  Harvey SA  Dooley CM  Bruijn E De  Eeden F Van  et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen.  Gills were harvested from four fish for each strain n=4  one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq  the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions.  Truseq stranded mRNA Assay. Paired end.,Experimental Factor: genotype:il10  / ,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP121190,Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills,ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16,FB18_S55_R1_001.fastq.gz FB18_S55_R2_001.fastq.gz,fastq fastq,4411576023.0,29389076.0,E MTAB 8958:FB18 S55 R,0:75.05 1:75.06,A:1153821133;C:1024593137;G:1029312154;T:1181989770;N:21859829,75,75,,,1153821133,1024593137,1029312154,1181989770,21859829,ERX4030556,ERS4514109,ERA2508092,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,UNIVERSITY OF MANCHESTER|European Nucleotide Archive,2,0.90933,0.90999,0.09581,0.09404,0.68917,0.69199,0.49527,0.49791,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United Kingdom,2020-04-16,Adult,Adult,Gill,Respiratory System
30673,SRR28233239,SRX23844453,SRS20664879,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b01,,strain:TRPA1b KO1|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b01,A1b01,A1b01,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1b-S1_1.fq.gz A1b-S1_2.fq.gz,fastq fastq,10214044500.0,34046815.0,A1b S1 1.fq.gz,0:150 1:150,A:2826731317;C:2254770618;G:2368382524;T:2764027721;N:132320,150,150,,,2826731317,2254770618,2368382524,2764027721,132320,SRX23844453,SRS20664879,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30674,SRR28233240,SRX23844452,SRS20664878,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT23,,strain:WT9|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT23,WT23,WT23,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-2-3_R1.fq.gz WT-2-3_R2.fq.gz,fastq fastq,6168655800.0,20562186.0,WT 2 3 R1.fq.gz,0:150 1:150,A:1556231017;C:1526432275;G:1545153210;T:1540414611;N:424687,150,150,,,1556231017,1526432275,1545153210,1540414611,424687,SRX23844452,SRS20664878,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30675,SRR28233241,SRX23844451,SRS20664877,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT22,,strain:WT8|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT22,WT22,WT22,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-2-2_R1.fq.gz WT-2-2_R2.fq.gz,fastq fastq,6503274900.0,21677583.0,WT 2 2 R1.fq.gz,0:150 1:150,A:1677274145;C:1574139629;G:1591639511;T:1659773624;N:447991,150,150,,,1677274145,1574139629,1591639511,1659773624,447991,SRX23844451,SRS20664877,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30676,SRR28233242,SRX23844450,SRS20664876,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT21,,strain:WT7|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT21,WT21,WT21,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-2-1_R1.fq.gz WT-2-1_R2.fq.gz,fastq fastq,6617487600.0,22058292.0,WT 2 1 R1.fq.gz,0:150 1:150,A:1701231328;C:1606849699;G:1625342674;T:1683607145;N:456754,150,150,,,1701231328,1606849699,1625342674,1683607145,456754,SRX23844450,SRS20664876,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30677,SRR28233243,SRX23844449,SRS20664875,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT13,,strain:WT6|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT13,WT13,WT13,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-1-3_R1.fq.gz WT-1-3_R2.fq.gz,fastq fastq,7102153500.0,23673845.0,WT 1 3 R1.fq.gz,0:150 1:150,A:1842496944;C:1707310744;G:1727403195;T:1824440904;N:501713,150,150,,,1842496944,1707310744,1727403195,1824440904,501713,SRX23844449,SRS20664875,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30678,SRR28233244,SRX23844448,SRS20664874,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT12,,strain:WT5|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT12,WT12,WT12,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-1-2_R1.fq.gz WT-1-2_R2.fq.gz,fastq fastq,6904290900.0,23014303.0,WT 1 2 R1.fq.gz,0:150 1:150,A:1794495968;C:1655549612;G:1677906470;T:1775860400;N:478450,150,150,,,1794495968,1655549612,1677906470,1775860400,478450,SRX23844448,SRS20664874,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30679,SRR28233245,SRX23844447,SRS20664873,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT11,,strain:WT4|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT11,WT11,WT11,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-1-1_R1.fq.gz WT-1-1_R2.fq.gz,fastq fastq,7005297000.0,23350990.0,WT 1 1 R1.fq.gz,0:150 1:150,A:1812285786;C:1684304098;G:1717096826;T:1791123167;N:487123,150,150,,,1812285786,1684304098,1717096826,1791123167,487123,SRX23844447,SRS20664873,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30680,SRR28233246,SRX23844446,SRS20664872,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT03,,strain:WT3|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT03,WT03,WT03,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-S3_1.fq.gz WT-S3_2.fq.gz,fastq fastq,5014921200.0,16716404.0,WT S3 1.fq.gz,0:150 1:150,A:1376105590;C:1123924635;G:1152769107;T:1361994867;N:127001,150,150,,,1376105590,1123924635,1152769107,1361994867,127001,SRX23844446,SRS20664872,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30681,SRR28233247,SRX23844445,SRS20664871,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b23,,strain:TRPA1b KO9|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b23,A1b23,A1b23,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1-2-3_R1.fq.gz A1-2-3_R2.fq.gz,fastq fastq,6844595700.0,22815319.0,A1 2 3 R1.fq.gz,0:150 1:150,A:1778935800;C:1644607281;G:1662211377;T:1758352025;N:489217,150,150,,,1778935800,1644607281,1662211377,1758352025,489217,SRX23844445,SRS20664871,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30682,SRR28233248,SRX23844444,SRS20664870,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b22,,strain:TRPA1b KO8|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b22,A1b22,A1b22,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1-2-2_R1.fq.gz A1-2-2_R2.fq.gz,fastq fastq,6529918800.0,21766396.0,A1 2 2 R1.fq.gz,0:150 1:150,A:1681524014;C:1580514490;G:1605344761;T:1662085103;N:450432,150,150,,,1681524014,1580514490,1605344761,1662085103,450432,SRX23844444,SRS20664870,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30683,SRR28233249,SRX23844443,SRS20664869,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b21,,strain:TRPA1b KO7|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b21,A1b21,A1b21,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1-2-1_R1.fq.gz A1-2-1_R2.fq.gz,fastq fastq,6836499600.0,22788332.0,A1 2 1 R1.fq.gz,0:150 1:150,A:1769098120;C:1648663116;G:1667962343;T:1750293771;N:482250,150,150,,,1769098120,1648663116,1667962343,1750293771,482250,SRX23844443,SRS20664869,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30684,SRR28233250,SRX23844442,SRS20664868,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b13,,strain:TRPA1b KO6|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b13,A1b13,A1b13,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1-1-3_R1.fq.gz A1-1-3_R2.fq.gz,fastq fastq,7024153800.0,23413846.0,A1 1 3 R1.fq.gz,0:150 1:150,A:1803658498;C:1704926954;G:1731475860;T:1783603775;N:488713,150,150,,,1803658498,1704926954,1731475860,1783603775,488713,SRX23844442,SRS20664868,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30685,SRR28233251,SRX23844441,SRS20664867,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b12,,strain:TRPA1b KO5|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b12,A1b12,A1b12,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1-1-2_R1.fq.gz A1-1-2_R2.fq.gz,fastq fastq,6764278200.0,22547594.0,A1 1 2 R1.fq.gz,0:150 1:150,A:1765465821;C:1610874768;G:1638217652;T:1749259791;N:460168,150,150,,,1765465821,1610874768,1638217652,1749259791,460168,SRX23844441,SRS20664867,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30686,SRR28233252,SRX23844440,SRS20664866,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b11,,strain:TRPA1b KO4|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b11,A1b11,A1b11,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1-1-1_R1.fq.gz A1-1-1_R2.fq.gz,fastq fastq,7001419800.0,23338066.0,A1 1 1 R1.fq.gz,0:150 1:150,A:1755052093;C:1727552789;G:1786513789;T:1731804911;N:496218,150,150,,,1755052093,1727552789,1786513789,1731804911,496218,SRX23844440,SRS20664866,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30687,SRR28233253,SRX23844439,SRS20664865,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b03,,strain:TRPA1b KO3|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b03,A1b03,A1b03,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1b-S3_1.fq.gz A1b-S3_2.fq.gz,fastq fastq,6656319000.0,22187730.0,A1b S3 1.fq.gz,0:150 1:150,A:1836354615;C:1486285665;G:1534973763;T:1798492449;N:212508,150,150,,,1836354615,1486285665,1534973763,1798492449,212508,SRX23844439,SRS20664865,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30688,SRR28233254,SRX23844438,SRS20664864,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,A1b02,,strain:TRPA1b KO2|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,A1b02,A1b02,A1b02,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,A1b-S2_1.fq.gz A1b-S2_2.fq.gz,fastq fastq,12350635200.0,41168784.0,A1b S2 1.fq.gz,0:150 1:150,A:3393503091;C:2740767056;G:2872562559;T:3343736443;N:66051,150,150,,,3393503091,2740767056,2872562559,3343736443,66051,SRX23844438,SRS20664864,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30689,SRR28233255,SRX23844437,SRS20664863,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT02,,strain:WT2|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT02,WT02,WT02,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-S2_1.fq.gz WT-S2_2.fq.gz,fastq fastq,6740391600.0,22467972.0,WT S2 1.fq.gz,0:150 1:150,A:1839600016;C:1523127157;G:1552667106;T:1824551017;N:446304,150,150,,,1839600016,1523127157,1552667106,1824551017,446304,SRX23844437,SRS20664863,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
30690,SRR28233256,SRX23844436,SRS20664862,SRP493528,PRJNA1084193,Knockout transcriptome sequencing of TRPA1b gene in zebrafish,PRJNA1084193,Other,WT and KO were sampled at the critical and half death time of room temperature and high temperature treatment  respectively.,,,,,WT01,,strain:WT1|age:4mpf|dev stage:adult|collection date:2024 01 20|geo loc name:China|sex:male|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,WT01,WT01,WT01,ribonucleic acid,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP493528,,,WT-S1_1.fq.gz WT-S1_2.fq.gz,fastq fastq,7104288900.0,23680963.0,WT S1 1.fq.gz,0:150 1:150,A:1946897695;C:1592125410;G:1641002833;T:1923739782;N:523180,150,150,,,1946897695,1592125410,1641002833,1923739782,523180,SRX23844436,SRS20664862,SRA1818205,Shanghai Ocean University|College of Aquaculture and Life Sciences,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-03-06,Adult,Adult,Gill,Respiratory System
31909,SRR28763300,SRX24328708,SRS21090012,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG27,,replicate name:12|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG27,EG27,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG27_1.fastq.gz EG27_2.fastq.gz,fastq fastq,9468037636.0,31351118.0,EG27 1.fastq.gz,0:151 1:151,A:2645026688;C:2045224768;G:2241526143;T:2536135792;N:124245,151,151,,,2645026688,2045224768,2241526143,2536135792,124245,SRX24328708,SRS21090012,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.96043,0.95691,0.0549,0.05519,0.8872,0.88791,0.91642,0.32446,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31910,SRR28763301,SRX24328707,SRS21090011,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG25,,replicate name:11|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG25,EG25,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG25_1.fastq.gz EG25_2.fastq.gz,fastq fastq,9880334680.0,32716340.0,EG25 1.fastq.gz,0:151 1:151,A:2794566002;C:2119943184;G:2295436572;T:2670257797;N:131125,151,151,,,2794566002,2119943184,2295436572,2670257797,131125,SRX24328707,SRS21090011,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.9497,0.94855,0.09296,0.09345,0.78577,0.78806,0.81265,0.81736,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31911,SRR28763302,SRX24328706,SRS21090010,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG23,,replicate name:10|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG23,EG23,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG23_2.fastq.gz EG23_1.fastq.gz,fastq fastq,9310716776.0,30830188.0,EG23 1.fastq.gz,0:151 1:151,A:2627699193;C:1989736585;G:2183889311;T:2509270699;N:120988,151,151,,,2627699193,1989736585,2183889311,2509270699,120988,SRX24328706,SRS21090010,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.95963,0.95589,0.06725,0.06923,0.89331,0.89514,0.92653,0.31643,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31912,SRR28763303,SRX24328705,SRS21090009,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG22,,replicate name:9|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG22,EG22,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG22_1.fastq.gz EG22_2.fastq.gz,fastq fastq,10098934662.0,33440181.0,EG22 1.fastq.gz,0:151 1:151,A:2849596303;C:2184335632;G:2385398269;T:2679468419;N:136039,151,151,,,2849596303,2184335632,2385398269,2679468419,136039,SRX24328705,SRS21090009,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.95966,0.95948,0.0597,0.06018,0.87724,0.87811,0.26587,0.30043,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31913,SRR28763304,SRX24328704,SRS21090008,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG21,,replicate name:8|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG21,EG21,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG21_2.fastq.gz EG21_1.fastq.gz,fastq fastq,9455903880.0,31310940.0,EG21 1.fastq.gz,0:151 1:151,A:2632664130;C:2047064096;G:2251422835;T:2524625050;N:127769,151,151,,,2632664130,2047064096,2251422835,2524625050,127769,SRX24328704,SRS21090008,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.94131,0.94159,0.09983,0.09968,0.83422,0.83473,0.81728,0.82964,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31914,SRR28763305,SRX24328703,SRS21090007,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG20,,replicate name:7|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG20,EG20,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG20_1.fastq.gz EG20_2.fastq.gz,fastq fastq,10208944504.0,33804452.0,EG20 1.fastq.gz,0:151 1:151,A:2904784539;C:2158820127;G:2293244638;T:2851958707;N:136493,151,151,,,2904784539,2158820127,2293244638,2851958707,136493,SRX24328703,SRS21090007,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.94799,0.95097,0.07416,0.07223,0.8591,0.86283,0.90914,0.28764,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31916,SRR28763307,SRX24328701,SRS21090005,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG19,,replicate name:6|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG19,EG19,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG19_1.fastq.gz EG19_2.fastq.gz,fastq fastq,10522416880.0,34842440.0,EG19 1.fastq.gz,0:151 1:151,A:2917044076;C:2328452801;G:2444054841;T:2832724906;N:140256,151,151,,,2917044076,2328452801,2444054841,2832724906,140256,SRX24328701,SRS21090005,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.95399,0.95401,0.07708,0.07832,0.82045,0.82171,0.74083,0.7189,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31917,SRR28763308,SRX24328700,SRS21090004,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG18,,replicate name:5|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 08|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG18,EG18,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG18_1.fastq.gz EG18_2.fastq.gz,fastq fastq,8756609894.0,28995397.0,EG18 1.fastq.gz,0:151 1:151,A:2511054564;C:1846539575;G:2028143579;T:2370754969;N:117207,151,151,,,2511054564,1846539575,2028143579,2370754969,117207,SRX24328700,SRS21090004,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.95603,0.95467,0.07502,0.07425,0.87547,0.87785,0.30779,0.29873,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31918,SRR28763309,SRX24328699,SRS21090003,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG17,,replicate name:4|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 08|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG17,EG17,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG17_1.fastq.gz EG17_2.fastq.gz,fastq fastq,10838410050.0,35888775.0,EG17 1.fastq.gz,0:151 1:151,A:3066998431;C:2291161659;G:2523979315;T:2956127087;N:143558,151,151,,,3066998431,2291161659,2523979315,2956127087,143558,SRX24328699,SRS21090003,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.94102,0.94248,0.10341,0.10249,0.82276,0.82479,0.86198,0.86305,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31919,SRR28763310,SRX24328698,SRS21090002,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG7,,replicate name:3|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG7,EG7,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG7_1.fastq.gz EG7_2.fastq.gz,fastq fastq,10125638408.0,33528604.0,EG7 1.fastq.gz,0:151 1:151,A:2685408022;C:2334564091;G:2564122607;T:2541408208;N:135480,151,151,,,2685408022,2334564091,2564122607,2541408208,135480,SRX24328698,SRS21090002,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.96855,0.96773,0.05197,0.05213,0.9124,0.91449,0.90093,0.90061,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31920,SRR28763311,SRX24328697,SRS21090001,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG6,,replicate name:2|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG6,EG6,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG6_1.fastq.gz EG6_2.fastq.gz,fastq fastq,8347409256.0,27640428.0,EG6 1.fastq.gz,0:151 1:151,A:2355233426;C:1773374207;G:1954779935;T:2263909727;N:111961,151,151,,,2355233426,1773374207,1954779935,2263909727,111961,SRX24328697,SRS21090001,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.95759,0.95489,0.06473,0.06571,0.88262,0.88428,0.92671,0.92842,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
31921,SRR28763312,SRX24328696,SRS21090000,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EG5,,replicate name:1|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio gill,EG5,EG5,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EG5_1.fastq.gz EG5_2.fastq.gz,fastq fastq,10544509086.0,34915593.0,EG5 1.fastq.gz,0:151 1:151,A:2929107857;C:2307092012;G:2499629363;T:2808538620;N:141234,151,151,,,2929107857,2307092012,2499629363,2808538620,141234,SRX24328696,SRS21090000,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.94866,0.9474,0.08636,0.08561,0.87545,0.87726,0.20035,0.88059,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Gill,Respiratory System
35967,SRR33391354,SRX28634187,SRS24905115,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV14D 2,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 27T08:05:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H120,H120,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_2_14d_gill.R1.fq ZB_SVCV_2_14d_gill.R2.fq,fastq fastq,6966025057.0,24131866.0,ZB SVCV 2 14d gill.R1.fq,0:144.33 1:144.34,A:1882860217;C:1593166410;G:1606066308;T:1883867275;N:64847,144,144,,,1882860217,1593166410,1606066308,1883867275,64847,SRX28634187,SRS24905115,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35968,SRR33391355,SRX28634186,SRS24905114,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV14D 1,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 27T08:00:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H119,H119,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_1_14d_gill.R1.fq ZB_SVCV_1_14d_gill.R2.fq,fastq fastq,6920780962.0,23788923.0,ZB SVCV 1 14d gill.R1.fq,0:145.45 1:145.47,A:1890441266;C:1564553550;G:1574656455;T:1891065927;N:63764,145,145,,,1890441266,1564553550,1574656455,1891065927,63764,SRX28634186,SRS24905114,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35969,SRR33391356,SRX28634185,SRS24905113,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV4D 4,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:35:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H118,H118,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_4_4d_gill.R1.fq ZB_SVCV_4_4d_gill.R2.fq,fastq fastq,6960662942.0,23947691.0,ZB SVCV 4 4d gill.R1.fq,0:145.31 1:145.35,A:1898230862;C:1576544417;G:1577166671;T:1908639715;N:81277,145,145,,,1898230862,1576544417,1577166671,1908639715,81277,SRX28634185,SRS24905113,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35970,SRR33391357,SRX28634184,SRS24905112,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV4D 3,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:30:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H117,H117,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_3_4d_gill.R1.fq ZB_SVCV_3_4d_gill.R2.fq,fastq fastq,6896551758.0,23694251.0,ZB SVCV 3 4d gill.R1.fq,0:145.51 1:145.55,A:1867347566;C:1574421227;G:1575481954;T:1879219305;N:81706,145,145,,,1867347566,1574421227,1575481954,1879219305,81706,SRX28634184,SRS24905112,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35971,SRR33391358,SRX28634183,SRS24905111,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV4D 2,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:25:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H116,H116,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_2_4d_gill.R1.fq ZB_SVCV_2_4d_gill.R2.fq,fastq fastq,6999980753.0,24085695.0,ZB SVCV 2 4d gill.R1.fq,0:145.29 1:145.34,A:1901052806;C:1592612390;G:1593603466;T:1912623714;N:88377,145,145,,,1901052806,1592612390,1593603466,1912623714,88377,SRX28634183,SRS24905111,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35972,SRR33391359,SRX28634182,SRS24905110,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV4D 1,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:20:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H115,H115,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_1_4d_gill.R1.fq ZB_SVCV_1_4d_gill.R2.fq,fastq fastq,7012033571.0,24052302.0,ZB SVCV 1 4d gill.R1.fq,0:145.74 1:145.79,A:1892650486;C:1606584045;G:1608404904;T:1904311435;N:82701,145,145,,,1892650486,1606584045,1608404904,1904311435,82701,SRX28634182,SRS24905110,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35973,SRR33391360,SRX28634181,SRS24905109,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,CON 4,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:15:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H114,H114,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_CON_4_gill.R1.fq ZB_CON_4_gill.R2.fq,fastq fastq,6929661185.0,24100208.0,ZB CON 4 gill.R1.fq,0:143.76 1:143.78,A:1877509781;C:1580761237;G:1592890100;T:1878437625;N:62442,143,143,,,1877509781,1580761237,1592890100,1878437625,62442,SRX28634181,SRS24905109,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35974,SRR33391361,SRX28634180,SRS24905108,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,CON 3,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:10:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H113,H113,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_CON_3_gill.R1.fq ZB_CON_3_gill.R2.fq,fastq fastq,7019729922.0,24395174.0,ZB CON 3 gill.R1.fq,0:143.86 1:143.89,A:1897770435;C:1606322507;G:1616884825;T:1898684128;N:68027,143,143,,,1897770435,1606322507,1616884825,1898684128,68027,SRX28634180,SRS24905108,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35975,SRR33391362,SRX28634179,SRS24905107,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV14D 4,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 27T08:15:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H122,H122,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_4_14d_gill.R1.fq ZB_SVCV_4_14d_gill.R2.fq,fastq fastq,6968038769.0,24268828.0,ZB SVCV 4 14d gill.R1.fq,0:143.55 1:143.57,A:1894155079;C:1584673108;G:1594301221;T:1894847261;N:62100,143,143,,,1894155079,1584673108,1594301221,1894847261,62100,SRX28634179,SRS24905107,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35976,SRR33391363,SRX28634178,SRS24905106,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,SVCV14D 3,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 27T08:10:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H121,H121,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_SVCV_3_14d_gill.R1.fq ZB_SVCV_3_14d_gill.R2.fq,fastq fastq,6951811490.0,24136855.0,ZB SVCV 3 14d gill.R1.fq,0:144.00 1:144.02,A:1852500638;C:1617829175;G:1627624953;T:1853792254;N:64470,144,144,,,1852500638,1617829175,1627624953,1853792254,64470,SRX28634178,SRS24905106,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35977,SRR33391364,SRX28634177,SRS24905105,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,CON 2,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:05:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H112,H112,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_CON_2_gill.R1.fq ZB_CON_2_gill.R2.fq,fastq fastq,7001642091.0,24194482.0,ZB CON 2 gill.R1.fq,0:144.69 1:144.70,A:1881759812;C:1611435897;G:1625551630;T:1882829975;N:64777,144,144,,,1881759812,1611435897,1625551630,1882829975,64777,SRX28634177,SRS24905105,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
35978,SRR33391365,SRX28634176,SRS24905104,SRP582507,PRJNA1256627,Danio rerio Raw sequence reads,PRJNA1256627,Whole Genome Sequencing,Compare the immune related pathways in the gill tissues of Danio rerio in the normal group and the SVCV infected group,,,,,CON 1,,strain:not applicable|isolate:not applicable|breed:AB WT|cultivar:not applicable|ecotype:not applicable|age:3 months|dev stage:not applicable|collection date:2025 01 17T08:00:00Z|geo loc name:China:Wuhan|sex:not collected|tissue:gill|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,H111,H111,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582507,,,ZB_CON_1_gill.R1.fq ZB_CON_1_gill.R2.fq,fastq fastq,6930336817.0,23773373.0,ZB CON 1 gill.R1.fq,0:145.73 1:145.79,A:1895505196;C:1565575763;G:1565751293;T:1903418631;N:85934,145,145,,,1895505196,1565575763,1565751293,1903418631,85934,SRX28634176,SRS24905104,SRA2121765,Huazhong Agricultural University|Fisheries College,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-04-30,Adult,Adult,Gill,Respiratory System
38065,SRR1524239,SRX661004,SRS665979,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish gills,Zebrafish gills,F Dr 3,,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,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,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,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
39612,SRR1873568,SRX915248,SRS870226,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,gills,GSM1630512,,source name:adult gills 1 year old|strain/background:AB|genotype/variation:wild type|tissue:gills|developmental stage:adult|age:1 year,gills,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult gills 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:gills|developmental stage:adult|age:1 year,GSM1630512,GSM1630512: gills; Danio rerio; miRNA Seq,GSM1630512,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630512,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,189248.0,3563.0,GSM1630512 r1,0:4 1:49.11,A:48212;C:55198;G:44765;T:40711;N:362,4,49,,,48212,55198,44765,40711,362,SRX915248,SRS870226,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,44,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Gill,Respiratory System
39705,SRR3579899,SRX1796667,SRS1464820,SRP059605,PRJNA287283,Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish,GSE69965,Other,Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit LTL  namely the lower end of survival temperature  is an important trait delimiting the geographical distribution of a species  however  the genetic mechanisms are poorly understood. We investigated the inter species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus  which were reared at a common temperature 28°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,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,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,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,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,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,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,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,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,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,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,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
44932,SRR6308290,SRX3408682,SRS2701478,SRP125291,PRJNA419036,Danio rerio strain:ASWT Transcriptome or Gene expression,PRJNA419036,Other,A genome wide map of circular RNA in adult zebrafish.,,,,Zf gills,Zf gills,,strain:ASWT|age:1year|sex:male|tissue:Gills|BioSampleModel:Model organism or animal,,,,,,,,,A genome wide map of circular RNA in adult zebrafish,Zf gills,Zf gills,Tissue were isolated from adult zebrafish anaesthetized using 0.004% Tricaine Sigma  USA. Extreme care was taken to avoid contamination to obtain pure homogenous tissue samples. The tissues were repeatedly washed in PBS to remove contaminating debris. The tissue samples were homogenized in Trizol for cell lysis Invitrogen  USA. RNA was isolated from the homogenized tissue samples using RNeasy kit Qiagen  USA. Sample preparation for sequencing was carried out using Truseq stranded RNA sample preparation kit Illumina  USA as per supplier's instructions. In order to remove the ribosomal RNA rRNA  one microgram of total RNA was hybridised with Ribo zero gold rRNA removal probe. Upon removing rRNA  the samples were processed for fragmentation in the presence of ionic cations at 37 degree Celcius. First stranded complementary DNA cDNA was prepared by random hexamers and superscript II reverse transcriptase Invitrogen  USA in presence of Actinomycin D to facilitate RNA dependent synthesis for improving strand specificity. The second strand was synthesised with second strand cDNA mix containing dUTP instead of dTTP and subjected to A base addition followed by adapter ligation. Final libraries were prepared by amplifying adapter ligated double strand cDNA. Clusters were generated on Hiseq flow cell v3 Illumina in cBot according to standard protocol Illumina USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125291,,,Zf_gills_R1.fastq Zf_gills_R2.fastq,fastq fastq,4496743848.0,22524306.0,Zf gills R2.fastq,0:99.98 1:99.65,A:1187180280;C:1050024773;G:1063872181;T:1195629658;N:36956,99,99,,,1187180280,1050024773,1063872181,1195629658,36956,SRX3408682,SRS2701478,SRA631861,CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine,CSIR-Institute of Genomics and Integrative Biology,2,0.79541,0.79749,0.21897,0.21816,0.68952,0.68947,0.50966,0.51356,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,ribozero,bulk,unknown,unknown,,India,2017-11-20,Adult,Adult,Gill,Respiratory System
53349,SRR9849251,SRX6603836,SRS5168885,SRP216556,PRJNA556842,aKlotho regulates age associated vascular calcification and lifespan in zebrafish,PRJNA556842,Transcriptome Analysis,The hormone aKlotho regulates lifespan in mice as knockouts die early of what appears to be accelerated aging due to hyperphosphatemia and soft tissue calcification. In contrast  its overexpression increases lifespan. Given the severe mouse phenotype  we generated zebrafish mutants for aklotho as well as its binding partner fibroblast growth factor 23 fgf23. Both mutations cause shortened lifespan in zebrafish  with abrupt onset of behavioral and degenerative physical changes at around five months of age. There is calcification of vessels throughout the body  most dramatically in the outflow tract of the heart  the bulbus arteriosus BA. This calcification is associated with ectopic activation of osteoclast differentiation pathways. These findings suggest that the gradual loss of aKlotho found in normal aging might give rise to ectopic calcification.,,,,αKlotho  gill  3 mpf  replicate 6,kl 14744 d gill,,strain:AB|age:3months|sex:female|tissue:gills|genotype:aKlotho|Replicate:Bilogical replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,Klotho  gill  3 mpf  replicate 6,kl 14744 d gill,kl 14744 d gill,Tissue collection and dissection: Adult zebrafish were euthanized by exposure to chilled water 0 4C. Gills  heart and kidney were collected from 32 individual fish at two time points  namely at 3 mpf and 5 mpf for klotho mutants and wildtype sibling controls AB background; 8 fish per genotype per time point   4 males  4 females for a total of 96 samples. Tissues were dissected in cold PBS and immediately stored in RNALater Stabilization Solution ThermoFisher Cat# AM7021. RNALater was removed post an overnight incubation at 4C  and samples were stored at  80C until processing. RNA extraction: All tissues were homogenized using the TissueLyser II Qiagen plus Lysis buffer containing  mercaptoethanol and stored at  80C. RNA extraction was performed using the automated protocol in the QIAcube workstation utilizing the RNeasy Fibrous Tissue Mini kit Qiagen Cat No./ID: 74704. RNA integrity and quality were assessed by Agilent TapeStation using High Sensitivity RNA ScreenTapes. Samples were normalized and 300ng of RNA was used for library prep for each sample. ERCC RNA Spike in mix was added for quality control. mRNA was captured using poly T oligos attached beads for library selection.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP216556,,,kl-14744-d-gill_merged_S63-1.fastq.gz kl-14744-d-gill_merged_S63-2.fastq.gz,fastq fastq,3202652208.0,21426652.0,kl 14744 d gill merged S63 1.fastq.gz,0:74.76 1:74.71,A:787284556;C:792881443;G:786148640;T:806832731;N:29504838,74,74,,,787284556,792881443,786148640,806832731,29504838,SRX6603836,SRS5168885,SRA927891,Novartis Institutes for Biomedical Research|Chemical Biology and Therapeutics,Novartis Institutes for Biomedical Research,2,0.95184,0.95423,0.08279,0.08221,0.6925,0.69244,0.50117,0.49895,75,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2019-07-27,Adult,Adult,Gill,Respiratory System
53350,SRR9849256,SRX6603835,SRS5168884,SRP216556,PRJNA556842,aKlotho regulates age associated vascular calcification and lifespan in zebrafish,PRJNA556842,Transcriptome Analysis,The hormone aKlotho regulates lifespan in mice as knockouts die early of what appears to be accelerated aging due to hyperphosphatemia and soft tissue calcification. In contrast  its overexpression increases lifespan. Given the severe mouse phenotype  we generated zebrafish mutants for aklotho as well as its binding partner fibroblast growth factor 23 fgf23. Both mutations cause shortened lifespan in zebrafish  with abrupt onset of behavioral and degenerative physical changes at around five months of age. There is calcification of vessels throughout the body  most dramatically in the outflow tract of the heart  the bulbus arteriosus BA. This calcification is associated with ectopic activation of osteoclast differentiation pathways. These findings suggest that the gradual loss of aKlotho found in normal aging might give rise to ectopic calcification.,,,,αKlotho  gill  3 mpf  replicate 7,kl 14744 f gill,,strain:AB|age:3months|sex:female|tissue:gills|genotype:aKlotho|Replicate:Bilogical replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,Klotho  gill  3 mpf  replicate 7,kl 14744 f gill,kl 14744 f gill,Tissue collection and dissection: Adult zebrafish were euthanized by exposure to chilled water 0 4C. Gills  heart and kidney were collected from 32 individual fish at two time points  namely at 3 mpf and 5 mpf for klotho mutants and wildtype sibling controls AB background; 8 fish per genotype per time point   4 males  4 females for a total of 96 samples. Tissues were dissected in cold PBS and immediately stored in RNALater Stabilization Solution ThermoFisher Cat# AM7021. RNALater was removed post an overnight incubation at 4C  and samples were stored at  80C until processing. RNA extraction: All tissues were homogenized using the TissueLyser II Qiagen plus Lysis buffer containing  mercaptoethanol and stored at  80C. RNA extraction was performed using the automated protocol in the QIAcube workstation utilizing the RNeasy Fibrous Tissue Mini kit Qiagen Cat No./ID: 74704. RNA integrity and quality were assessed by Agilent TapeStation using High Sensitivity RNA ScreenTapes. Samples were normalized and 300ng of RNA was used for library prep for each sample. ERCC RNA Spike in mix was added for quality control. mRNA was captured using poly T oligos attached beads for library selection.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP216556,,,kl-14744-f-gill_merged_S28-1.fastq.gz kl-14744-f-gill_merged_S28-2.fastq.gz,fastq fastq,3290448619.0,22023416.0,kl 14744 f gill merged S28 1.fastq.gz,0:74.72 1:74.69,A:852051739;C:772110143;G:764138186;T:870831842;N:31316709,74,74,,,852051739,772110143,764138186,870831842,31316709,SRX6603835,SRS5168884,SRA927891,Novartis Institutes for Biomedical Research|Chemical Biology and Therapeutics,Novartis Institutes for Biomedical Research,2,0.93891,0.94218,0.11083,0.10988,0.68682,0.68732,0.51269,0.51959,76,74,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2019-07-27,Adult,Adult,Gill,Respiratory System
53351,SRR9849252,SRX6603834,SRS5168883,SRP216556,PRJNA556842,aKlotho regulates age associated vascular calcification and lifespan in zebrafish,PRJNA556842,Transcriptome Analysis,The hormone aKlotho regulates lifespan in mice as knockouts die early of what appears to be accelerated aging due to hyperphosphatemia and soft tissue calcification. In contrast  its overexpression increases lifespan. Given the severe mouse phenotype  we generated zebrafish mutants for aklotho as well as its binding partner fibroblast growth factor 23 fgf23. Both mutations cause shortened lifespan in zebrafish  with abrupt onset of behavioral and degenerative physical changes at around five months of age. There is calcification of vessels throughout the body  most dramatically in the outflow tract of the heart  the bulbus arteriosus BA. This calcification is associated with ectopic activation of osteoclast differentiation pathways. These findings suggest that the gradual loss of aKlotho found in normal aging might give rise to ectopic calcification.,,,,αKlotho  gill  3 mpf  replicate 8,kl 14744 h gill,,strain:AB|age:3months|sex:female|tissue:gills|genotype:aKlotho|Replicate:Bilogical replicate 8|BioSampleModel:Model organism or animal,,,,,,,,,Klotho  gill  3 mpf  replicate 8,kl 14744 h gill,kl 14744 h gill,Tissue collection and dissection: Adult zebrafish were euthanized by exposure to chilled water 0 4C. Gills  heart and kidney were collected from 32 individual fish at two time points  namely at 3 mpf and 5 mpf for klotho mutants and wildtype sibling controls AB background; 8 fish per genotype per time point   4 males  4 females for a total of 96 samples. Tissues were dissected in cold PBS and immediately stored in RNALater Stabilization Solution ThermoFisher Cat# AM7021. RNALater was removed post an overnight incubation at 4C  and samples were stored at  80C until processing. RNA extraction: All tissues were homogenized using the TissueLyser II Qiagen plus Lysis buffer containing  mercaptoethanol and stored at  80C. RNA extraction was performed using the automated protocol in the QIAcube workstation utilizing the RNeasy Fibrous Tissue Mini kit Qiagen Cat No./ID: 74704. RNA integrity and quality were assessed by Agilent TapeStation using High Sensitivity RNA ScreenTapes. Samples were normalized and 300ng of RNA was used for library prep for each sample. ERCC RNA Spike in mix was added for quality control. mRNA was captured using poly T oligos attached beads for library selection.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP216556,,,kl-14744-h-gill_merged_S88-1.fastq.gz kl-14744-h-gill_merged_S88-2.fastq.gz,fastq fastq,2993191869.0,20020896.0,kl 14744 h gill merged S88 1.fastq.gz,0:74.77 1:74.73,A:745064408;C:729194088;G:729776159;T:761918449;N:27238765,74,74,,,745064408,729194088,729776159,761918449,27238765,SRX6603834,SRS5168883,SRA927891,Novartis Institutes for Biomedical Research|Chemical Biology and Therapeutics,Novartis Institutes for Biomedical Research,2,0.94847,0.95062,0.08456,0.08377,0.6942,0.69576,0.51192,0.51533,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2019-07-27,Adult,Adult,Gill,Respiratory System
53352,SRR9849255,SRX6603833,SRS5168882,SRP216556,PRJNA556842,aKlotho regulates age associated vascular calcification and lifespan in zebrafish,PRJNA556842,Transcriptome Analysis,The hormone aKlotho regulates lifespan in mice as knockouts die early of what appears to be accelerated aging due to hyperphosphatemia and soft tissue calcification. In contrast  its overexpression increases lifespan. Given the severe mouse phenotype  we generated zebrafish mutants for aklotho as well as its binding partner fibroblast growth factor 23 fgf23. Both mutations cause shortened lifespan in zebrafish  with abrupt onset of behavioral and degenerative physical changes at around five months of age. There is calcification of vessels throughout the body  most dramatically in the outflow tract of the heart  the bulbus arteriosus BA. This calcification is associated with ectopic activation of osteoclast differentiation pathways. These findings suggest that the gradual loss of aKlotho found in normal aging might give rise to ectopic calcification.,,,,αKlotho  gill  5 mpf  replicate 1,kl 14562 a gill,,strain:AB|age:5months|sex:male|tissue:gills|genotype:aKlotho|Replicate:Bilogical replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,Klotho  gill  5 mpf  replicate 1,kl 14562 a gill,kl 14562 a gill,Tissue collection and dissection: Adult zebrafish were euthanized by exposure to chilled water 0 4C. Gills  heart and kidney were collected from 32 individual fish at two time points  namely at 3 mpf and 5 mpf for klotho mutants and wildtype sibling controls AB background; 8 fish per genotype per time point   4 males  4 females for a total of 96 samples. Tissues were dissected in cold PBS and immediately stored in RNALater Stabilization Solution ThermoFisher Cat# AM7021. RNALater was removed post an overnight incubation at 4C  and samples were stored at  80C until processing. RNA extraction: All tissues were homogenized using the TissueLyser II Qiagen plus Lysis buffer containing  mercaptoethanol and stored at  80C. RNA extraction was performed using the automated protocol in the QIAcube workstation utilizing the RNeasy Fibrous Tissue Mini kit Qiagen Cat No./ID: 74704. RNA integrity and quality were assessed by Agilent TapeStation using High Sensitivity RNA ScreenTapes. Samples were normalized and 300ng of RNA was used for library prep for each sample. ERCC RNA Spike in mix was added for quality control. mRNA was captured using poly T oligos attached beads for library selection.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP216556,,,kl-14562-a-gill_merged_S62-1.fastq.gz kl-14562-a-gill_merged_S62-2.fastq.gz,fastq fastq,4948315549.0,33026008.0,kl 14562 a gill merged S62 1.fastq.gz,0:74.93 1:74.90,A:1264379777;C:1187097302;G:1173849990;T:1292353460;N:30635020,74,74,,,1264379777,1187097302,1173849990,1292353460,30635020,SRX6603833,SRS5168882,SRA927891,Novartis Institutes for Biomedical Research|Chemical Biology and Therapeutics,Novartis Institutes for Biomedical Research,2,0.94579,0.9481,0.10417,0.10358,0.69118,0.69179,0.49146,0.50019,76,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2019-07-27,Adult,Adult,Gill,Respiratory System
53353,SRR9849253,SRX6603832,SRS5168881,SRP216556,PRJNA556842,aKlotho regulates age associated vascular calcification and lifespan in zebrafish,PRJNA556842,Transcriptome Analysis,The hormone aKlotho regulates lifespan in mice as knockouts die early of what appears to be accelerated aging due to hyperphosphatemia and soft tissue calcification. In contrast  its overexpression increases lifespan. Given the severe mouse phenotype  we generated zebrafish mutants for aklotho as well as its binding partner fibroblast growth factor 23 fgf23. Both mutations cause shortened lifespan in zebrafish  with abrupt onset of behavioral and degenerative physical changes at around five months of age. There is calcification of vessels throughout the body  most dramatically in the outflow tract of the heart  the bulbus arteriosus BA. This calcification is associated with ectopic activation of osteoclast differentiation pathways. These findings suggest that the gradual loss of aKlotho found in normal aging might give rise to ectopic calcification.,,,,αKlotho  gill  5 mpf  replicate 2,kl 14563 a gill,,strain:AB|age:5months|sex:male|tissue:gills|genotype:aKlotho|Replicate:Bilogical replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,Klotho  gill  5 mpf  replicate 2,kl 14563 a gill,kl 14563 a gill,Tissue collection and dissection: Adult zebrafish were euthanized by exposure to chilled water 0 4C. Gills  heart and kidney were collected from 32 individual fish at two time points  namely at 3 mpf and 5 mpf for klotho mutants and wildtype sibling controls AB background; 8 fish per genotype per time point   4 males  4 females for a total of 96 samples. Tissues were dissected in cold PBS and immediately stored in RNALater Stabilization Solution ThermoFisher Cat# AM7021. RNALater was removed post an overnight incubation at 4C  and samples were stored at  80C until processing. RNA extraction: All tissues were homogenized using the TissueLyser II Qiagen plus Lysis buffer containing  mercaptoethanol and stored at  80C. RNA extraction was performed using the automated protocol in the QIAcube workstation utilizing the RNeasy Fibrous Tissue Mini kit Qiagen Cat No./ID: 74704. RNA integrity and quality were assessed by Agilent TapeStation using High Sensitivity RNA ScreenTapes. Samples were normalized and 300ng of RNA was used for library prep for each sample. ERCC RNA Spike in mix was added for quality control. mRNA was captured using poly T oligos attached beads for library selection.,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP216556,,,kl-14563-a-gill_merged_S26-1.fastq.gz kl-14563-a-gill_merged_S26-2.fastq.gz,fastq fastq,4105985705.0,27689417.0,kl 14563 a gill merged S26 1.fastq.gz,0:74.15 1:74.14,A:1073116772;C:944775687;G:934585663;T:1094337784;N:59169799,74,74,,,1073116772,944775687,934585663,1094337784,59169799,SRX6603832,SRS5168881,SRA927891,Novartis Institutes for Biomedical Research|Chemical Biology and Therapeutics,Novartis Institutes for Biomedical Research,2,0.93325,0.93593,0.1444,0.14317,0.68858,0.68878,0.5035,0.50318,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2019-07-27,Adult,Adult,Gill,Respiratory System