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
25304,SRR25793376,SRX21515638,SRS18742880,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144    adult,miR 144 adult,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 1,144 1 adult blood,144 1 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144AL1_S10.fastq,fastq,781435052.0,17368946.0,DC 144AL1 S10.fastq,0:44.99,A:207445570;C:148430622;G:177122903;T:245179579;N:3256378,44,,,,207445570,148430622,177122903,245179579,3256378,SRX21515638,SRS18742880,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.8759,,0.28126,,0.95051,,0.47905,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25305,SRR25793377,SRX21515637,SRS18742882,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type   adult,WT adult,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 3,WT3 adult blood,WT3 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTA3_S6.fastq,fastq,601997398.0,17290043.0,DC WTA3 S6.fastq,0:34.82,A:136034449;C:142779447;G:177204517;T:134955264;N:11023721,34,,,,136034449,142779447,177204517,134955264,11023721,SRX21515637,SRS18742882,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.32909,,0.08525,,0.95288,,0.60214,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25306,SRR25793378,SRX21515636,SRS18742882,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type   adult,WT adult,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 2,WT2 adult blood,WT2 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTA2_S5.fastq,fastq,669871903.0,17381581.0,DC WTA2 S5.fastq,0:38.54,A:169704437;C:140964096;G:160484620;T:189596855;N:9121895,38,,,,169704437,140964096,160484620,189596855,9121895,SRX21515636,SRS18742882,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.69865,,0.19099,,0.93432,,0.47502,,68,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25307,SRR25793379,SRX21515635,SRS18742882,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type   adult,WT adult,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 1,WT1 adult blood,WT1 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTA1_S4.fastq,fastq,824193699.0,17465379.0,DC WTA1 S4.fastq,0:47.19,A:209553199;C:169966117;G:194322860;T:244145525;N:6205998,47,,,,209553199,169966117,194322860,244145525,6205998,SRX21515635,SRS18742882,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.76241,,0.25975,,0.94619,,0.50211,,66,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25308,SRR25793380,SRX21515634,SRS18742881,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144    embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 3,144 3 embryo blood,144 3 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144EL3_S18.fastq,fastq,687309797.0,17039739.0,DC 144EL3 S18.fastq,0:40.34,A:159186558;C:130452893;G:155820002;T:181676510;N:60173834,40,,,,159186558,130452893,155820002,181676510,60173834,SRX21515634,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.52966,,0.16941,,0.97615,,0.58418,,61,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25309,SRR25793381,SRX21515633,SRS18742881,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144    embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 2,144 2 embryo blood,144 2 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144EL2_S17.fastq,fastq,495318731.0,14459195.0,DC 144EL2 S17.fastq,0:34.26,A:110392869;C:106378418;G:128881687;T:107956679;N:41709078,34,,,,110392869,106378418,128881687,107956679,41709078,SRX21515633,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.32147,,0.04496,,0.97569,,0.58512,,31,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25310,SRR25793382,SRX21515632,SRS18742881,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144    embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 1,144 1 embryo blood,144 1 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144EL1_S16.fastq,fastq,974854100.0,20079553.0,DC 144EL1 S16.fastq,0:48.55,A:233861010;C:192987350;G:215192262;T:269960344;N:62853134,48,,,,233861010,192987350,215192262,269960344,62853134,SRX21515632,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.77953,,0.18084,,0.90905,,0.74157,,75,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25311,SRR25793383,SRX21515631,SRS18742879,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type   embryo,WT embryo,,isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 3,WT3 embryo blood,WT3 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTE3_S15.fastq,fastq,657139116.0,15618072.0,DC WTE3 S15.fastq,0:42.08,A:154495614;C:122942896;G:147719345;T:179403193;N:52578068,42,,,,154495614,122942896,147719345,179403193,52578068,SRX21515631,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.56358,,0.19381,,0.96757,,0.6115,,76,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25312,SRR25793384,SRX21515630,SRS18742880,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144    adult,miR 144 adult,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 3,144 3 adult blood,144 3 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144AL3_S12.fastq,fastq,498938612.0,14861511.0,DC 144AL3 S12.fastq,0:33.57,A:137243823;C:96735877;G:109220779;T:152042235;N:3695898,33,,,,137243823,96735877,109220779,152042235,3695898,SRX21515630,SRS18742880,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.82213,,0.16617,,0.95053,,0.46386,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25313,SRR25793385,SRX21515629,SRS18742880,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144    adult,miR 144 adult,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 2,144 2 adult blood,144 2 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144AL2_S11.fastq,fastq,497890134.0,10636306.0,DC 144AL2 S11.fastq,0:46.81,A:134598214;C:94036725;G:109501897;T:158719603;N:1033695,46,,,,134598214,94036725,109501897,158719603,1033695,SRX21515629,SRS18742880,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.88496,,0.29132,,0.96002,,0.53343,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System
25314,SRR25793386,SRX21515628,SRS18742879,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type   embryo,WT embryo,,isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 2,WT2 embryo blood,WT2 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTE2_S14.fastq,fastq,250958009.0,9755304.0,DC WTE2 S14.fastq,0:25.73,A:43225839;C:41823862;G:54150092;T:43159724;N:68598492,25,,,,43225839,41823862,54150092,43159724,68598492,SRX21515628,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.34114,,0.05466,,0.96664,,0.54625,,47,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25315,SRR25793387,SRX21515627,SRS18742879,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type   embryo,WT embryo,,isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 1,WT1 embryo blood,WT1 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTE1_S13.fastq,fastq,816518564.0,19556325.0,DC WTE1 S13.fastq,0:41.75,A:187091550;C:151287428;G:179967901;T:221475884;N:76695801,41,,,,187091550,151287428,179967901,221475884,76695801,SRX21515627,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.61681,,0.1874,,0.95101,,0.56879,,29,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
38293,SRR1647684,SRX756919,SRS742121,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,24S,GSM1541908,,source name:spleen|tissue:spleen|disease state:24h post SVCV infection,24S,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata 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: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|disease state:24h post SVCV infection,GSM1541908,GSM1541908: 24S; Danio rerio; RNA Seq,GSM1541908,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541908,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,24S_ATGTCA_L003_R1.fastq,fastq,1207014756.0,23666956.0,GSM1541908 r1,0:51,A:316359100;C:290453604;G:283305513;T:316815698;N:80841,51,,,,316359100,290453604,283305513,316815698,80841,SRX756919,SRS742121,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.91158,,0.09021,,0.70867,,0.46907,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Spleen,Hematopoietic System
38294,SRR1647683,SRX756918,SRS742119,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,6S,GSM1541907,,source name:spleen|tissue:spleen|disease state:6h post SVCV infection,6S,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata 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: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|disease state:6h post SVCV infection,GSM1541907,GSM1541907: 6S; Danio rerio; RNA Seq,GSM1541907,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541907,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,6S_AGTTCC_L003_R1.fastq,fastq,1251006540.0,24529540.0,GSM1541907 r1,0:51,A:323805792;C:303846999;G:297418642;T:325862442;N:72665,51,,,,323805792,303846999,297418642,325862442,72665,SRX756918,SRS742119,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92105,,0.09005,,0.71273,,0.46937,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Spleen,Hematopoietic System
38295,SRR1647682,SRX756917,SRS742118,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,0S,GSM1541906,,source name:spleen|tissue:spleen|disease state:un infected,0S,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata 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: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|disease state:un infected,GSM1541906,GSM1541906: 0S; Danio rerio; RNA Seq,GSM1541906,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541906,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,0S_AGTCAA_L003_R1.fastq,fastq,1155087372.0,22648772.0,GSM1541906 r1,0:51,A:301183546;C:279328135;G:272663981;T:301834798;N:76912,51,,,,301183546,279328135,272663981,301834798,76912,SRX756917,SRS742118,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.91841,,0.09679,,0.70546,,0.47624,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Spleen,Hematopoietic System
39665,SRR2027911,SRX1029315,SRS937775,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,GSM1686459,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686459,GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq,GSM1686459,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686459,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz,fastq,988427889.0,19380939.0,GSM1686459 r1,0:51,A:322268594;C:166925867;G:171531103;T:327506982;N:195343,51,,,,322268594,166925867,171531103,327506982,195343,SRX1029315,SRS937775,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.6999,,0.24019,,0.85358,,0.56832,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39666,SRR2027910,SRX1029314,SRS937773,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,GSM1686458,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686458,GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq,GSM1686458,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686458,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz,fastq,846771207.0,16603357.0,GSM1686458 r1,0:51,A:268435928;C:150903620;G:153931870;T:273331733;N:168056,51,,,,268435928,150903620,153931870,273331733,168056,SRX1029314,SRS937773,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72025,,0.17943,,0.87937,,0.5683,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39667,SRR2027909,SRX1029313,SRS937774,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,GSM1686457,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686457,GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq,GSM1686457,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686457,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz,fastq,807459642.0,15832542.0,GSM1686457 r1,0:51,A:260516660;C:140425216;G:145411663;T:260942267;N:163836,51,,,,260516660,140425216,145411663,260942267,163836,SRX1029313,SRS937774,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.7097,,0.17187,,0.93304,,0.64092,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39668,SRR2027908,SRX1029312,SRS937776,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,GSM1686456,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686456,GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq,GSM1686456,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686456,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz,fastq,1523483526.0,29872226.0,GSM1686456 r1,0:51,A:499019794;C:267493952;G:277264815;T:479405699;N:299266,51,,,,499019794,267493952,277264815,479405699,299266,SRX1029312,SRS937776,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.67328,,0.15117,,0.91179,,0.54858,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39669,SRR2027907,SRX1029311,SRS937777,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,GSM1686455,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686455,GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq,GSM1686455,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686455,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz,fastq,938675094.0,18405394.0,GSM1686455 r1,0:51,A:284384359;C:173449465;G:178039777;T:302612825;N:188668,51,,,,284384359,173449465,178039777,302612825,188668,SRX1029311,SRS937777,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72884,,0.14723,,0.90767,,0.57414,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39670,SRR2027906,SRX1029310,SRS937778,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,GSM1686454,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686454,GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq,GSM1686454,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686454,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz,fastq,1248324348.0,24476948.0,GSM1686454 r1,0:51,A:391067882;C:223380294;G:229132022;T:404526410;N:217740,51,,,,391067882,223380294,229132022,404526410,217740,SRX1029310,SRS937778,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.70232,,0.14257,,0.92894,,0.59305,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39974,SRR2726604,SRX1354695,SRS1121101,SRP064895,PRJNA298967,Danio rerio Raw sequence reads,PRJNA298967,Whole Genome Sequencing,Alternative polyadenylation in the anti bacterial immune response of zebrafish,,,,,UC.fq.gz,,breed:missing|cultivar:missing|ecotype:missing|isolate:missing|strain:missing|age:6 month|dev stage:adult|sex:male|tissue:spleen|BioSampleModel:Model organism or animal,,,,,,,,,Alternative polyadenylation in the anti bacterial immune response of zebrafish,UC,298967,SAPAS three prime cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP064895,,,UC.fq.gz,fastq,908330752.0,16220192.0,UC,0:56,A:268296300;C:164753303;G:152582935;T:321764605;N:933609,56,,,,268296300,164753303,152582935,321764605,933609,SRX1354695,SRS1121101,SRA305678,"Sun Yat-Sen University|Department of Biochemistry, College of Life Scienc",Sun Yat-Sen University,1,0.76113,,0.14836,,0.86764,,0.49191,,56,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2015-10-19,Adult,Adult,Spleen,Hematopoietic System
39975,SRR2726605,SRX1343023,SRS1117908,SRP064895,PRJNA298967,Danio rerio Raw sequence reads,PRJNA298967,Whole Genome Sequencing,Alternative polyadenylation in the anti bacterial immune response of zebrafish,,,,,BC.fq.gz,,breed:missing|cultivar:missing|ecotype:missing|isolate:missing|strain:missing|age:6 month|dev stage:adult|sex:male|tissue:spleen|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal,,,,,,,,,Alternative polyadenylation in the anti bacterial immune response of zebrafish,298967,298967,SAPAS three prime cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP064895,,,BC.fq.gz,fastq,613456536.0,10954581.0,BC,0:56,A:184952368;C:111595938;G:99647506;T:216155456;N:1105268,56,,,,184952368,111595938,99647506,216155456,1105268,SRX1343023,SRS1117908,SRA305678,"Sun Yat-Sen University|Department of Biochemistry, College of Life Scienc",Sun Yat-Sen University,1,0.74636,,0.11848,,0.84678,,0.47133,,56,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2015-10-24,Adult,Adult,Spleen,Hematopoietic System
41032,SRR3581739,SRX1797279,SRS1465200,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting3,C NF3,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF3,C NF3,C NF3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF3.fastq.gz,fastq,1745512893.0,34225743.0,C NF3.fastq.gz,0:51,A:470456301;C:396221813;G:401458508;T:477287506;N:88765,51,,,,470456301,396221813,401458508,477287506,88765,SRX1797279,SRS1465200,SRA429046,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.92839,,0.06821,,0.73099,,0.44395,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-05-25,Larval,Larval,Blood,Hematopoietic System
41033,SRR3581729,SRX1797278,SRS1465199,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting2,C NF2,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF2,C NF2,C NF2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF2.fastq.gz,fastq,2116510506.0,41500206.0,C NF2.fastq.gz,0:51,A:580244434;C:475940957;G:474848964;T:585459729;N:16422,51,,,,580244434,475940957,474848964,585459729,16422,SRX1797278,SRS1465199,SRA429045,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.90388,,0.06926,,0.78963,,0.49501,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
41034,SRR3581718,SRX1797274,SRS1465196,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting1,C NF1,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF1,C NF1,C NF1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF1.fastq.gz,fastq,1492422690.0,29263190.0,C NF1.fastq.gz,0:51,A:421145406;C:327412398;G:328273236;T:415327504;N:264146,51,,,,421145406,327412398,328273236,415327504,264146,SRX1797274,SRS1465196,SRA429041,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.82347,,0.08561,,0.75207,,0.45637,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
41038,SRR3581671,SRX1797269,SRS1465191,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Fluorescence activated cell sorted macrophages1,iRed1,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages|BioSampleModel:Model organism or animal,,,,,,,,,iRed1,iRed1,iRed1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,iRed1.fastq.gz,fastq,2227229772.0,43671172.0,iRed1.fastq.gz,0:51,A:643185725;C:477251583;G:480258902;T:626515881;N:17681,51,,,,643185725,477251583,480258902,626515881,17681,SRX1797269,SRS1465191,SRA429036,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.88005,,0.11318,,0.76197,,0.49474,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System
41039,SRR3581670,SRX1797268,SRS1465190,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma5,disGran5,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran5,disGran5,disGran5,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran5.fastq.gz,fastq,2097698850.0,41131350.0,disGran5.fastq.gz,0:51,A:606466942;C:449212134;G:448063993;T:593938942;N:16839,51,,,,606466942,449212134,448063993,593938942,16839,SRX1797268,SRS1465190,SRA429035,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.89212,,0.09154,,0.76788,,0.51096,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System
41040,SRR3581669,SRX1797267,SRS1465187,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma4,disGran4,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran4,disGran4,disGran4,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran4.fastq.gz,fastq,2969920485.0,58233735.0,disGran4.fastq.gz,0:51,A:861895830;C:635643178;G:635675729;T:836681349;N:24399,51,,,,861895830,635643178,635675729,836681349,24399,SRX1797267,SRS1465187,SRA429034,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.87215,,0.09876,,0.7498,,0.55116,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System
41041,SRR3581668,SRX1797266,SRS1465186,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma3,disGran3,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran3,disGran3,disGran3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran3.fastq.gz,fastq,2398905207.0,47037357.0,disGran3.fastq.gz,0:51,A:693817641;C:513302774;G:516121702;T:675643798;N:19292,51,,,,693817641,513302774,516121702,675643798,19292,SRX1797266,SRS1465186,SRA429033,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.88631,,0.10719,,0.75465,,0.51255,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System
41042,SRR3581667,SRX1797265,SRS1465185,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma2,disGran2,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran2,disGran2,disGran2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran2.fastq.gz,fastq,2108649213.0,41346063.0,disGran2.fastq.gz,0:51,A:606624392;C:457029369;G:459017347;T:585961261;N:16844,51,,,,606624392,457029369,459017347,585961261,16844,SRX1797265,SRS1465185,SRA429032,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.88259,,0.10405,,0.74282,,0.536,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System
41043,SRR3581315,SRX1797076,SRS1465045,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma1,disGran1,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran1,disGran1,disGran1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran1.fastq.gz,fastq,2529627234.0,49600534.0,disGran1.fastq.gz,0:51,A:738849065;C:530442613;G:521673896;T:738641232;N:20428,51,,,,738849065,530442613,521673896,738641232,20428,SRX1797076,SRS1465045,SRA428910,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.81713,,0.09754,,0.75213,,0.51283,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-07-24,Adult,Adult,Blood,Hematopoietic System
47583,SRR6661157,SRX3638253,SRS2904504,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWTPHZ 3,GSM2975201,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWTPHZ 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975201,GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq,GSM2975201,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975201,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWTPHZ_3.fastq.gz,fastq,863137362.0,16924262.0,GSM2975201 r1,0:51,A:243029420;C:186621398;G:190769119;T:242704294;N:13131,51,,,,243029420,186621398,190769119,242704294,13131,SRX3638253,SRS2904504,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94871,,0.18797,,0.7289,,0.48689,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47584,SRR6661156,SRX3638252,SRS2904503,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWTPHZ 2,GSM2975200,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWTPHZ 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975200,GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq,GSM2975200,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975200,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWTPHZ_2.fastq.gz,fastq,748057494.0,14667794.0,GSM2975200 r1,0:51,A:212731080;C:159238564;G:163993235;T:212082953;N:11662,51,,,,212731080,159238564,163993235,212082953,11662,SRX3638252,SRS2904503,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94641,,0.22364,,0.7264,,0.48998,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47585,SRR6661155,SRX3638251,SRS2904502,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWTPHZ 1,GSM2975199,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWTPHZ 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975199,GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq,GSM2975199,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975199,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWTPHZ_1.fastq.gz,fastq,771862917.0,15134567.0,GSM2975199 r1,0:51,A:220317243;C:164032479;G:167543123;T:219958265;N:11807,51,,,,220317243,164032479,167543123,219958265,11807,SRX3638251,SRS2904502,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94835,,0.1926,,0.71453,,0.48677,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47586,SRR6661154,SRX3638250,SRS2904501,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWT 3,GSM2975198,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWT 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975198,GSM2975198: SplWT 3; Danio rerio; RNA Seq,GSM2975198,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975198,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWT_3.fastq.gz,fastq,815973888.0,15999488.0,GSM2975198 r1,0:51,A:236186435;C:169473350;G:175246943;T:235055142;N:12018,51,,,,236186435,169473350,175246943,235055142,12018,SRX3638250,SRS2904501,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94554,,0.25855,,0.71873,,0.54675,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47587,SRR6661153,SRX3638249,SRS2904499,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWT 2,GSM2975197,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWT 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975197,GSM2975197: SplWT 2; Danio rerio; RNA Seq,GSM2975197,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975197,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWT_2.fastq.gz,fastq,909644262.0,17836162.0,GSM2975197 r1,0:51,A:259661486;C:192636111;G:198048163;T:259284494;N:14008,51,,,,259661486,192636111,198048163,259284494,14008,SRX3638249,SRS2904499,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94781,,0.22979,,0.69962,,0.49839,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47588,SRR6661152,SRX3638248,SRS2904500,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWT 1,GSM2975196,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWT 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975196,GSM2975196: SplWT 1; Danio rerio; RNA Seq,GSM2975196,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975196,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWT_1.fastq.gz,fastq,888755274.0,17426574.0,GSM2975196 r1,0:51,A:241072815;C:200347978;G:205733626;T:241587449;N:13406,51,,,,241072815,200347978,205733626,241587449,13406,SRX3638248,SRS2904500,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.95759,,0.1342,,0.72918,,0.52233,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47589,SRR6661151,SRX3638247,SRS2904498,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKOPHZ 3,GSM2975195,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKOPHZ 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975195,GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq,GSM2975195,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975195,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKOPHZ_3.fastq.gz,fastq,881441160.0,17283160.0,GSM2975195 r1,0:51,A:243254581;C:194198200;G:199055092;T:244919975;N:13312,51,,,,243254581,194198200,199055092,244919975,13312,SRX3638247,SRS2904498,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.90441,,0.14881,,0.71447,,0.51129,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47590,SRR6661150,SRX3638246,SRS2904497,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKOPHZ 2,GSM2975194,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKOPHZ 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975194,GSM2975194: SplDKOPHZ 2; Danio rerio; RNA Seq,GSM2975194,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975194,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKOPHZ_2.fastq.gz,fastq,795840414.0,15604714.0,GSM2975194 r1,0:51,A:229921467;C:166126021;G:170186584;T:229594266;N:12076,51,,,,229921467,166126021,170186584,229594266,12076,SRX3638246,SRS2904497,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.88657,,0.23556,,0.7194,,0.51207,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47591,SRR6661149,SRX3638245,SRS2904495,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKOPHZ 1,GSM2975193,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKOPHZ 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975193,GSM2975193: SplDKOPHZ 1; Danio rerio; RNA Seq,GSM2975193,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975193,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKOPHZ_1.fastq.gz,fastq,788951436.0,15469636.0,GSM2975193 r1,0:51,A:217408862;C:175236911;G:178930271;T:217363444;N:11948,51,,,,217408862,175236911,178930271,217363444,11948,SRX3638245,SRS2904495,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.90945,,0.10065,,0.72468,,0.48596,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47592,SRR6661148,SRX3638244,SRS2904496,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKO 3,GSM2975192,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKO 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975192,GSM2975192: SplDKO 3; Danio rerio; RNA Seq,GSM2975192,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975192,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKO_3.fastq.gz,fastq,732609543.0,14364893.0,GSM2975192 r1,0:51,A:209020386;C:154988652;G:160405898;T:208183578;N:11029,51,,,,209020386,154988652,160405898,208183578,11029,SRX3638244,SRS2904496,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.88228,,0.23609,,0.72529,,0.50392,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47593,SRR6661147,SRX3638243,SRS2904493,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKO 2,GSM2975191,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKO 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975191,GSM2975191: SplDKO 2; Danio rerio; RNA Seq,GSM2975191,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975191,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKO_2.fastq.gz,fastq,747985635.0,14666385.0,GSM2975191 r1,0:51,A:209892939;C:160527969;G:165683955;T:211869190;N:11582,51,,,,209892939,160527969,165683955,211869190,11582,SRX3638243,SRS2904493,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.90267,,0.20054,,0.7249,,0.53668,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47594,SRR6661146,SRX3638242,SRS2904494,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKO 1,GSM2975190,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKO 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975190,GSM2975190: SplDKO 1; Danio rerio; RNA Seq,GSM2975190,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975190,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKO_1.fastq.gz,fastq,724574391.0,14207341.0,GSM2975190 r1,0:51,A:207549130;C:151913145;G:156789401;T:208311727;N:10988,51,,,,207549130,151913145,156789401,208311727,10988,SRX3638242,SRS2904494,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.89742,,0.2275,,0.71547,,0.5072,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
49748,SRR8040452,SRX4870965,SRS3925946,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps5 RNA seq,GSM3427234,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps5 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427234,GSM3427234: t32lps5 RNA seq; Danio rerio; RNA Seq,GSM3427234,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427234,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2525095950.0,33667946.0,GSM3427234 r1,0:75 1:0,A:654325529;C:574214700;G:560979222;T:735543925;N:32574,75,0,,,654325529,574214700,560979222,735543925,32574,SRX4870965,SRS3925946,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94279,,0.11158,,0.7739,,0.56131,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49749,SRR8040451,SRX4870964,SRS3925945,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps4 RNA seq,GSM3427233,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427233,GSM3427233: t32lps4 RNA seq; Danio rerio; RNA Seq,GSM3427233,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427233,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2324475900.0,30993012.0,GSM3427233 r1,0:75 1:0,A:593299460;C:533734154;G:526980483;T:670430972;N:30831,75,0,,,593299460,533734154,526980483,670430972,30831,SRX4870964,SRS3925945,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.9455,,0.10812,,0.78046,,0.55958,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49750,SRR8040450,SRX4870962,SRS3925943,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps3 RNA seq,GSM3427232,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427232,GSM3427232: t32lps3 RNA seq; Danio rerio; RNA Seq,GSM3427232,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427232,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2390945250.0,31879270.0,GSM3427232 r1,0:75 1:0,A:620617289;C:546536575;G:538087155;T:685671110;N:33121,75,0,,,620617289,546536575,538087155,685671110,33121,SRX4870962,SRS3925943,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94216,,0.12594,,0.74925,,0.54113,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49751,SRR8040449,SRX4870961,SRS3925942,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps2 RNA seq,GSM3427231,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427231,GSM3427231: t32lps2 RNA seq; Danio rerio; RNA Seq,GSM3427231,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427231,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2372211900.0,31629492.0,GSM3427231 r1,0:75 1:0,A:609244327;C:553579722;G:546387461;T:662968297;N:32093,75,0,,,609244327,553579722,546387461,662968297,32093,SRX4870961,SRS3925942,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91064,,0.09975,,0.7318,,0.52325,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49752,SRR8040448,SRX4870960,SRS3925941,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps1 RNA seq,GSM3427230,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427230,GSM3427230: t32lps1 RNA seq; Danio rerio; RNA Seq,GSM3427230,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427230,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2601300000.0,34684000.0,GSM3427230 r1,0:75 1:0,A:696279292;C:582818011;G:571718581;T:750447755;N:36361,75,0,,,696279292,582818011,571718581,750447755,36361,SRX4870960,SRS3925941,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93957,,0.13624,,0.74641,,0.53521,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49753,SRR8040447,SRX4870959,SRS3925940,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct10 RNA seq,GSM3427229,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct10 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427229,GSM3427229: t32ct10 RNA seq; Danio rerio; RNA Seq,GSM3427229,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427229,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2206367925.0,29418239.0,GSM3427229 r1,0:75 1:0,A:564695219;C:513292663;G:507293808;T:621057423;N:28812,75,0,,,564695219,513292663,507293808,621057423,28812,SRX4870959,SRS3925940,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94594,,0.10744,,0.75511,,0.39959,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49754,SRR8040446,SRX4870958,SRS3925939,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct8 RNA seq,GSM3427228,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427228,GSM3427228: t32ct8 RNA seq; Danio rerio; RNA Seq,GSM3427228,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427228,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2160654900.0,28808732.0,GSM3427228 r1,0:75 1:0,A:560268124;C:491395956;G:494788088;T:614174312;N:28420,75,0,,,560268124,491395956,494788088,614174312,28420,SRX4870958,SRS3925939,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91437,,0.1131,,0.74661,,0.54441,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49755,SRR8040445,SRX4870957,SRS3925938,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct6 RNA seq,GSM3427227,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct6 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427227,GSM3427227: t32ct6 RNA seq; Danio rerio; RNA Seq,GSM3427227,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427227,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2175448725.0,29005983.0,GSM3427227 r1,0:75 1:0,A:588911336;C:487829921;G:471925092;T:626753522;N:28854,75,0,,,588911336,487829921,471925092,626753522,28854,SRX4870957,SRS3925938,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93789,,0.14514,,0.73839,,0.51589,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49756,SRR8040444,SRX4870956,SRS3925937,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct3 RNA seq,GSM3427226,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427226,GSM3427226: t32ct3 RNA seq; Danio rerio; RNA Seq,GSM3427226,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427226,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2350450425.0,31339339.0,GSM3427226 r1,0:75 1:0,A:612558543;C:533417342;G:511898107;T:692543546;N:32887,75,0,,,612558543,533417342,511898107,692543546,32887,SRX4870956,SRS3925937,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.88939,,0.13696,,0.74649,,0.5071,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49757,SRR8040443,SRX4870955,SRS3925936,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct2 RNA seq,GSM3427225,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427225,GSM3427225: t32ct2 RNA seq; Danio rerio; RNA Seq,GSM3427225,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427225,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2500728150.0,33343042.0,GSM3427225 r1,0:75 1:0,A:663109698;C:565815864;G:564300306;T:707468578;N:33704,75,0,,,663109698,565815864,564300306,707468578,33704,SRX4870955,SRS3925936,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92821,,0.27272,,0.71969,,0.48781,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49758,SRR8040442,SRX4870954,SRS3925988,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps8 RNA seq,GSM3427224,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427224,GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq,GSM3427224,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427224,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2342903700.0,31238716.0,GSM3427224 r1,0:75 1:0,A:613986696;C:535703169;G:527411229;T:665771221;N:31385,75,0,,,613986696,535703169,527411229,665771221,31385,SRX4870954,SRS3925988,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92238,,0.11108,,0.75223,,0.54609,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49759,SRR8040441,SRX4870953,SRS3925935,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps4 RNA seq,GSM3427223,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427223,GSM3427223: t28lps4 RNA seq; Danio rerio; RNA Seq,GSM3427223,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427223,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2009201550.0,26789354.0,GSM3427223 r1,0:75 1:0,A:503118595;C:466998217;G:461838042;T:577221133;N:25563,75,0,,,503118595,466998217,461838042,577221133,25563,SRX4870953,SRS3925935,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.85044,,0.10362,,0.78149,,0.59209,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49760,SRR8040440,SRX4870952,SRS3925934,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps3 RNA seq,GSM3427222,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427222,GSM3427222: t28lps3 RNA seq; Danio rerio; RNA Seq,GSM3427222,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427222,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2262918375.0,30172245.0,GSM3427222 r1,0:75 1:0,A:557712391;C:559312209;G:525961809;T:619902191;N:29775,75,0,,,557712391,559312209,525961809,619902191,29775,SRX4870952,SRS3925934,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.75792,,0.0861,,0.77977,,0.47016,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49761,SRR8040439,SRX4870951,SRS3925933,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps2 RNA seq,GSM3427221,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427221,GSM3427221: t28lps2 RNA seq; Danio rerio; RNA Seq,GSM3427221,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427221,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2362744425.0,31503259.0,GSM3427221 r1,0:75 1:0,A:605359081;C:550864600;G:543725417;T:662762619;N:32708,75,0,,,605359081,550864600,543725417,662762619,32708,SRX4870951,SRS3925933,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92027,,0.10164,,0.7403,,0.52342,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49762,SRR8040438,SRX4870950,SRS3925932,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps1 RNA seq,GSM3427220,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427220,GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq,GSM3427220,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427220,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2219433000.0,29592440.0,GSM3427220 r1,0:75 1:0,A:559427934;C:519857518;G:513429485;T:626687457;N:30606,75,0,,,559427934,519857518,513429485,626687457,30606,SRX4870950,SRS3925932,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.89861,,0.09731,,0.76889,,0.4978,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49763,SRR8040437,SRX4870949,SRS3925931,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct7 RNA seq,GSM3427219,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct7 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427219,GSM3427219: t28ct7 RNA seq; Danio rerio; RNA Seq,GSM3427219,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427219,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2329584075.0,31061121.0,GSM3427219 r1,0:75 1:0,A:624440550;C:517755267;G:499439713;T:687917841;N:30704,75,0,,,624440550,517755267,499439713,687917841,30704,SRX4870949,SRS3925931,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.88755,,0.13982,,0.75739,,0.56552,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49764,SRR8040436,SRX4870948,SRS3925930,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct5 RNA seq,GSM3427218,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct5 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427218,GSM3427218: t28ct5 RNA seq; Danio rerio; RNA Seq,GSM3427218,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427218,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2116347225.0,28217963.0,GSM3427218 r1,0:75 1:0,A:549735276;C:488049942;G:477129323;T:601405177;N:27507,75,0,,,549735276,488049942,477129323,601405177,27507,SRX4870948,SRS3925930,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94198,,0.11445,,0.75487,,0.53068,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49765,SRR8040435,SRX4870947,SRS3925929,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct3 RNA seq,GSM3427217,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427217,GSM3427217: t28ct3 RNA seq; Danio rerio; RNA Seq,GSM3427217,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427217,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2689388775.0,35858517.0,GSM3427217 r1,0:75 1:0,A:723021338;C:600600385;G:595495733;T:770233672;N:37647,75,0,,,723021338,600600385,595495733,770233672,37647,SRX4870947,SRS3925929,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.9433,,0.12005,,0.75175,,0.52805,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49766,SRR8040434,SRX4870946,SRS3925927,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct2 RNA seq,GSM3427216,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427216,GSM3427216: t28ct2 RNA seq; Danio rerio; RNA Seq,GSM3427216,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427216,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2358123450.0,31441646.0,GSM3427216 r1,0:75 1:0,A:608599109;C:548957677;G:537939593;T:662594226;N:32845,75,0,,,608599109,548957677,537939593,662594226,32845,SRX4870946,SRS3925927,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93343,,0.09904,,0.73701,,0.50221,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49767,SRR8040433,SRX4870945,SRS3925928,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct1 RNA seq,GSM3427215,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427215,GSM3427215: t28ct1 RNA seq; Danio rerio; RNA Seq,GSM3427215,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427215,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2340413625.0,31205515.0,GSM3427215 r1,0:75 1:0,A:601455783;C:547481954;G:534319560;T:657124045;N:32283,75,0,,,601455783,547481954,534319560,657124045,32283,SRX4870945,SRS3925928,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91963,,0.11224,,0.7363,,0.52602,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49768,SRR8040432,SRX4870944,SRS3925926,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps8 RNA seq,GSM3427214,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427214,GSM3427214: t24lps8 RNA seq; Danio rerio; RNA Seq,GSM3427214,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427214,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,1914339900.0,25524532.0,GSM3427214 r1,0:75 1:0,A:512209644;C:432894621;G:420067370;T:549142945;N:25320,75,0,,,512209644,432894621,420067370,549142945,25320,SRX4870944,SRS3925926,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92034,,0.12782,,0.73777,,0.53097,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49769,SRR8040431,SRX4870943,SRS3925925,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps4 RNA seq,GSM3427213,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427213,GSM3427213: t24lps4 RNA seq; Danio rerio; RNA Seq,GSM3427213,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427213,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2137202850.0,28496038.0,GSM3427213 r1,0:75 1:0,A:542475947;C:498947754;G:490366774;T:605383850;N:28525,75,0,,,542475947,498947754,490366774,605383850,28525,SRX4870943,SRS3925925,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91347,,0.09882,,0.75763,,0.46833,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49770,SRR8040430,SRX4870942,SRS3925924,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps3 RNA seq,GSM3427212,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427212,GSM3427212: t24lps3 RNA seq; Danio rerio; RNA Seq,GSM3427212,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427212,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2514206700.0,33522756.0,GSM3427212 r1,0:75 1:0,A:663829025;C:573707517;G:558298485;T:718336661;N:35012,75,0,,,663829025,573707517,558298485,718336661,35012,SRX4870942,SRS3925924,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93997,,0.11968,,0.74241,,0.53459,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49771,SRR8040429,SRX4870941,SRS3925923,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps2 RNA seq,GSM3427211,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427211,GSM3427211: t24lps2 RNA seq; Danio rerio; RNA Seq,GSM3427211,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427211,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2502607650.0,33368102.0,GSM3427211 r1,0:75 1:0,A:659207653;C:572452612;G:556598074;T:714314698;N:34613,75,0,,,659207653,572452612,556598074,714314698,34613,SRX4870941,SRS3925923,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92032,,0.12899,,0.7441,,0.52707,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49772,SRR8040428,SRX4870940,SRS3925921,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps1 RNA seq,GSM3427210,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427210,GSM3427210: t24lps1 RNA seq; Danio rerio; RNA Seq,GSM3427210,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427210,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2301013650.0,30680182.0,GSM3427210 r1,0:75 1:0,A:600014931;C:531214958;G:529006695;T:640746698;N:30368,75,0,,,600014931,531214958,529006695,640746698,30368,SRX4870940,SRS3925921,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94819,,0.10959,,0.74706,,0.44871,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49773,SRR8040427,SRX4870939,SRS3925922,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24ct8 RNA seq,GSM3427209,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24ct8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427209,GSM3427209: t24ct8 RNA seq; Danio rerio; RNA Seq,GSM3427209,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427209,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2196418725.0,29285583.0,GSM3427209 r1,0:75 1:0,A:573278624;C:504375268;G:494497295;T:624238861;N:28677,75,0,,,573278624,504375268,494497295,624238861,28677,SRX4870939,SRS3925922,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94225,,0.11903,,0.75051,,0.55244,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49774,SRR8040426,SRX4870938,SRS3925919,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24ct5 RNA seq,GSM3427208,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24ct5 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427208,GSM3427208: t24ct5 RNA seq; Danio rerio; RNA Seq,GSM3427208,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427208,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2267199975.0,30229333.0,GSM3427208 r1,0:75 1:0,A:584789099;C:523482900;G:517770578;T:641127463;N:29935,75,0,,,584789099,523482900,517770578,641127463,29935,SRX4870938,SRS3925919,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.88505,,0.11534,,0.74566,,0.55279,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49775,SRR8040425,SRX4870937,SRS3925920,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24ct4 RNA seq,GSM3427207,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24ct4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427207,GSM3427207: t24ct4 RNA seq; Danio rerio; RNA Seq,GSM3427207,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427207,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2127502425.0,28366699.0,GSM3427207 r1,0:75 1:0,A:543019165;C:503067510;G:498801425;T:582586507;N:27818,75,0,,,543019165,503067510,498801425,582586507,27818,SRX4870937,SRS3925920,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.9223,,0.07915,,0.72401,,0.51588,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49776,SRR8040424,SRX4870936,SRS3925917,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24ct3 RNA seq,GSM3427206,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24ct3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427206,GSM3427206: t24ct3 RNA seq; Danio rerio; RNA Seq,GSM3427206,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427206,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2708072025.0,36107627.0,GSM3427206 r1,0:75 1:0,A:672991238;C:642923577;G:634295347;T:757824608;N:37255,75,0,,,672991238,642923577,634295347,757824608,37255,SRX4870936,SRS3925917,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.95238,,0.09,,0.75513,,0.52869,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49777,SRR8040423,SRX4870935,SRS3925918,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24ct2 RNA seq,GSM3427205,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24ct2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427205,GSM3427205: t24ct2 RNA seq; Danio rerio; RNA Seq,GSM3427205,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427205,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2495119875.0,33268265.0,GSM3427205 r1,0:75 1:0,A:627918584;C:589525055;G:590001770;T:687639074;N:35392,75,0,,,627918584,589525055,590001770,687639074,35392,SRX4870935,SRS3925918,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.95519,,0.08888,,0.74746,,0.44744,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49778,SRR8040485,SRX4870997,SRS3925977,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps7 miRNA seq,GSM3427264,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps7 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427264,GSM3427264: t32lps7 miRNA seq; Danio rerio; miRNA Seq,GSM3427264,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427264,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,2979410976.0,39202776.0,GSM3427264 r1,0:76 1:0,A:680890914;C:823795284;G:813206458;T:661494032;N:24288,76,0,,,680890914,823795284,813206458,661494032,24288,SRX4870997,SRS3925977,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00172,,0.00036,,0.99659,,0.5774,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49779,SRR8040484,SRX4870996,SRS3925976,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps5 miRNA seq,GSM3427263,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps5 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427263,GSM3427263: t32lps5 miRNA seq; Danio rerio; miRNA Seq,GSM3427263,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427263,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,3748512888.0,49322538.0,GSM3427263 r1,0:76 1:0,A:827904249;C:957754082;G:980630416;T:982193588;N:30553,76,0,,,827904249,957754082,980630416,982193588,30553,SRX4870996,SRS3925976,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00336,,0.00087,,0.99657,,0.58597,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49780,SRR8040483,SRX4870995,SRS3925975,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps3 miRNA seq,GSM3427262,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps3 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427262,GSM3427262: t32lps3 miRNA seq; Danio rerio; miRNA Seq,GSM3427262,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427262,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,738838712.0,9721562.0,GSM3427262 r1,0:76 1:0,A:153616530;C:205779426;G:206416216;T:173020629;N:5911,76,0,,,153616530,205779426,206416216,173020629,5911,SRX4870995,SRS3925975,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.01547,,0.00084,,0.99614,,0.65654,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49781,SRR8040482,SRX4870994,SRS3925974,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps2 miRNA seq,GSM3427261,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps2 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427261,GSM3427261: t32lps2 miRNA seq; Danio rerio; miRNA Seq,GSM3427261,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427261,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,826032068.0,10868843.0,GSM3427261 r1,0:76 1:0,A:173874245;C:231864336;G:237091534;T:183195515;N:6438,76,0,,,173874245,231864336,237091534,183195515,6438,SRX4870994,SRS3925974,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00642,,0.00032,,0.99799,,0.64507,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49782,SRR8040481,SRX4870993,SRS3925973,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps1 miRNA seq,GSM3427260,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps1 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427260,GSM3427260: t32lps1 miRNA seq; Danio rerio; miRNA Seq,GSM3427260,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427260,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,939595752.0,12363102.0,GSM3427260 r1,0:76 1:0,A:208106865;C:264360671;G:242572550;T:224548001;N:7665,76,0,,,208106865,264360671,242572550,224548001,7665,SRX4870993,SRS3925973,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00675,,0.00042,,0.99776,,0.6162,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49783,SRR8040480,SRX4870992,SRS3925972,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct9 miRNA seq,GSM3427259,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct9 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427259,GSM3427259: t32ct9 miRNA seq; Danio rerio; miRNA Seq,GSM3427259,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427259,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,2182814316.0,28721241.0,GSM3427259 r1,0:76 1:0,A:538572480;C:545202669;G:589186456;T:509834541;N:18170,76,0,,,538572480,545202669,589186456,509834541,18170,SRX4870992,SRS3925972,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00546,,0.00069,,0.99466,,0.54142,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49784,SRR8040479,SRX4870991,SRS3925971,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct8 miRNA seq,GSM3427258,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct8 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427258,GSM3427258: t32ct8 miRNA seq; Danio rerio; miRNA Seq,GSM3427258,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427258,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1782092536.0,23448586.0,GSM3427258 r1,0:76 1:0,A:374737718;C:453267098;G:524775360;T:429298160;N:14200,76,0,,,374737718,453267098,524775360,429298160,14200,SRX4870991,SRS3925971,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.01211,,0.00262,,0.99322,,0.61785,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49785,SRR8040478,SRX4870990,SRS3925970,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct7 miRNA seq,GSM3427257,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct7 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427257,GSM3427257: t32ct7 miRNA seq; Danio rerio; miRNA Seq,GSM3427257,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427257,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1276775908.0,16799683.0,GSM3427257 r1,0:76 1:0,A:293029271;C:327721470;G:322223336;T:333791186;N:10645,76,0,,,293029271,327721470,322223336,333791186,10645,SRX4870990,SRS3925970,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00721,,0.00121,,0.99691,,0.60335,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49786,SRR8040477,SRX4870989,SRS3925969,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct6 miRNA seq,GSM3427256,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct6 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427256,GSM3427256: t32ct6 miRNA seq; Danio rerio; miRNA Seq,GSM3427256,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427256,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,865696012.0,11390737.0,GSM3427256 r1,0:76 1:0,A:176770645;C:244509184;G:239312533;T:205096390;N:7260,76,0,,,176770645,244509184,239312533,205096390,7260,SRX4870989,SRS3925969,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.01202,,0.00047,,0.99685,,0.63568,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49787,SRR8040476,SRX4870988,SRS3925968,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct3 miRNA seq,GSM3427255,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct3 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427255,GSM3427255: t32ct3 miRNA seq; Danio rerio; miRNA Seq,GSM3427255,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427255,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,682433716.0,8979391.0,GSM3427255 r1,0:76 1:0,A:124505314;C:191879438;G:199861760;T:166181598;N:5606,76,0,,,124505314,191879438,199861760,166181598,5606,SRX4870988,SRS3925968,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00115,,0.00016,,0.99766,,0.63905,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49788,SRR8040475,SRX4870987,SRS3925966,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps8 miRNA seq,GSM3427254,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps8 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427254,GSM3427254: t28lps8 miRNA seq; Danio rerio; miRNA Seq,GSM3427254,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427254,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1616866180.0,21274555.0,GSM3427254 r1,0:76 1:0,A:318698931;C:431888920;G:467466474;T:398799027;N:12828,76,0,,,318698931,431888920,467466474,398799027,12828,SRX4870987,SRS3925966,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00516,,0.00033,,0.99805,,0.60541,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49789,SRR8040474,SRX4870986,SRS3926099,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps5 miRNA seq,GSM3427253,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps5 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427253,GSM3427253: t28lps5 miRNA seq; Danio rerio; miRNA Seq,GSM3427253,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427253,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,685130044.0,9014869.0,GSM3427253 r1,0:76 1:0,A:157108408;C:176642434;G:187178331;T:164195292;N:5579,76,0,,,157108408,176642434,187178331,164195292,5579,SRX4870986,SRS3926099,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.01486,,0.00126,,0.99547,,0.61029,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49790,SRR8040473,SRX4870985,SRS3925965,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps4 miRNA seq,GSM3427252,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps4 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427252,GSM3427252: t28lps4 miRNA seq; Danio rerio; miRNA Seq,GSM3427252,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427252,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1939474552.0,25519402.0,GSM3427252 r1,0:76 1:0,A:360469874;C:575927354;G:555750389;T:447311541;N:15394,76,0,,,360469874,575927354,555750389,447311541,15394,SRX4870985,SRS3925965,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00727,,0.00123,,0.9948,,0.57604,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49791,SRR8040472,SRX4870984,SRS3925964,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps2 miRNA seq,GSM3427251,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps2 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427251,GSM3427251: t28lps2 miRNA seq; Danio rerio; miRNA Seq,GSM3427251,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427251,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1099817964.0,14471289.0,GSM3427251 r1,0:76 1:0,A:243156900;C:278653612;G:304671994;T:273326443;N:9015,76,0,,,243156900,278653612,304671994,273326443,9015,SRX4870984,SRS3925964,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.01845,,0.0012,,0.99671,,0.58128,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49792,SRR8040471,SRX4870983,SRS3925963,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps1 miRNA seq,GSM3427250,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps1 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427250,GSM3427250: t28lps1 miRNA seq; Danio rerio; miRNA Seq,GSM3427250,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427250,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,448779772.0,5904997.0,GSM3427250 r1,0:76 1:0,A:90816279;C:135297788;G:114875760;T:107786041;N:3904,76,0,,,90816279,135297788,114875760,107786041,3904,SRX4870983,SRS3925963,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.03409,,0.00322,,0.99371,,0.59951,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49793,SRR8040470,SRX4870982,SRS3925961,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct7 miRNA seq,GSM3427249,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct7 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427249,GSM3427249: t28ct7 miRNA seq; Danio rerio; miRNA Seq,GSM3427249,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427249,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,385887644.0,5077469.0,GSM3427249 r1,0:76 1:0,A:87709108;C:102972334;G:97802557;T:97400488;N:3157,76,0,,,87709108,102972334,97802557,97400488,3157,SRX4870982,SRS3925961,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.03137,,0.00448,,0.99354,,0.64505,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49794,SRR8040469,SRX4870981,SRS3925960,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct5 miRNA seq,GSM3427248,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct5 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427248,GSM3427248: t28ct5 miRNA seq; Danio rerio; miRNA Seq,GSM3427248,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427248,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,530506600.0,6980350.0,GSM3427248 r1,0:76 1:0,A:116331973;C:147098854;G:132744863;T:134326464;N:4446,76,0,,,116331973,147098854,132744863,134326464,4446,SRX4870981,SRS3925960,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.0176,,0.0022,,0.99586,,0.65278,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49795,SRR8040468,SRX4870980,SRS3926000,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct3 miRNA seq,GSM3427247,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct3 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427247,GSM3427247: t28ct3 miRNA seq; Danio rerio; miRNA Seq,GSM3427247,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427247,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,854083592.0,11237942.0,GSM3427247 r1,0:76 1:0,A:207803970;C:226907346;G:210770016;T:208595483;N:6777,76,0,,,207803970,226907346,210770016,208595483,6777,SRX4870980,SRS3926000,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00898,,0.00088,,0.99685,,0.55397,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49796,SRR8040467,SRX4870979,SRS3925959,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct2 miRNA seq,GSM3427246,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct2 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427246,GSM3427246: t28ct2 miRNA seq; Danio rerio; miRNA Seq,GSM3427246,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427246,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1344896988.0,17696013.0,GSM3427246 r1,0:76 1:0,A:281151040;C:362525663;G:337235896;T:363973330;N:11059,76,0,,,281151040,362525663,337235896,363973330,11059,SRX4870979,SRS3925959,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00513,,0.00084,,0.99748,,0.572,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49797,SRR8040466,SRX4870978,SRS3925998,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct1 miRNA seq,GSM3427245,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct1 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427245,GSM3427245: t28ct1 miRNA seq; Danio rerio; miRNA Seq,GSM3427245,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427245,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,1092530324.0,14375399.0,GSM3427245 r1,0:76 1:0,A:223117238;C:311189912;G:305409606;T:252804765;N:8803,76,0,,,223117238,311189912,305409606,252804765,8803,SRX4870978,SRS3925998,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00305,,0.00045,,0.99722,,0.55111,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49798,SRR8040465,SRX4870977,SRS3925958,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps8 miRNA seq,GSM3427244,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps8 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427244,GSM3427244: t24lps8 miRNA seq; Danio rerio; miRNA Seq,GSM3427244,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427244,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,883122736.0,11620036.0,GSM3427244 r1,0:76 1:0,A:173839280;C:249832164;G:243138214;T:216305485;N:7593,76,0,,,173839280,249832164,243138214,216305485,7593,SRX4870977,SRS3925958,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00807,,0.00098,,0.99466,,0.58038,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49799,SRR8040464,SRX4870976,SRS3925957,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps6 miRNA seq,GSM3427243,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps6 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427243,GSM3427243: t24lps6 miRNA seq; Danio rerio; miRNA Seq,GSM3427243,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427243,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,940200788.0,12371063.0,GSM3427243 r1,0:76 1:0,A:202186441;C:257211490;G:262526872;T:218268364;N:7621,76,0,,,202186441,257211490,262526872,218268364,7621,SRX4870976,SRS3925957,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.01545,,0.00138,,0.99573,,0.63229,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49800,SRR8040463,SRX4870975,SRS3925956,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps3 miRNA seq,GSM3427242,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps3 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427242,GSM3427242: t24lps3 miRNA seq; Danio rerio; miRNA Seq,GSM3427242,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427242,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,563241168.0,7411068.0,GSM3427242 r1,0:76 1:0,A:122781441;C:156393075;G:148935008;T:135126829;N:4815,76,0,,,122781441,156393075,148935008,135126829,4815,SRX4870975,SRS3925956,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.04539,,0.00261,,0.99245,,0.45999,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49801,SRR8040462,SRX4870974,SRS3925955,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps2 miRNA seq,GSM3427241,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps2 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427241,GSM3427241: t24lps2 miRNA seq; Danio rerio; miRNA Seq,GSM3427241,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427241,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,847700960.0,11153960.0,GSM3427241 r1,0:76 1:0,A:188114093;C:239338523;G:228371307;T:191870154;N:6883,76,0,,,188114093,239338523,228371307,191870154,6883,SRX4870974,SRS3925955,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.03556,,0.00381,,0.98959,,0.60491,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49802,SRR8040461,SRX4870973,SRS3925954,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps1 miRNA seq,GSM3427240,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps1 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427240,GSM3427240: t24lps1 miRNA seq; Danio rerio; miRNA Seq,GSM3427240,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427240,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,808775888.0,10641788.0,GSM3427240 r1,0:76 1:0,A:180792047;C:227912694;G:210745152;T:189319125;N:6870,76,0,,,180792047,227912694,210745152,189319125,6870,SRX4870973,SRS3925954,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.03455,,0.00417,,0.99265,,0.6371,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49803,SRR8040460,SRX4870972,SRS3925953,SRP165278,PRJNA495918,Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish,GSE121164,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three temperature groups 24 °C  28 °C  32 °C for incubation. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures  32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs  adjusted p value < 0.05  |fold change| > 2.0  DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C  3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a  including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24ct9 miRNA seq,GSM3427239,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24ct9 miRNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish  another 15 teleost species Astatotilapia burtoni  Cyprinus carpio  Electrophorus electricus  Fugu rubripes  Gadus morhua  Hippoglossus hippoglossus  Ictalurus punctatus  Metrizclima zebra  Neolamprologus brichardi  Oryzias latipes  Oreochromis niloticus  Pundamilia nyererei  Paralichthys olivaceus  Salmo salar  Tetraodon nigroviridis and three model species Drosophila melanogaster  Mus musculus  Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA  rRNA  snRNA  snoRNA were filterred out  and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427239,GSM3427239: t24ct9 miRNA seq; Danio rerio; miRNA Seq,GSM3427239,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some changes. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific  USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially  and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min  1 cycle; 95 °C for 20 s  60 °C for 30 s  72 °C for 15 s  22 cycles; 72 °C for 2 min  1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427239,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP165278,,,,,936832772.0,12326747.0,GSM3427239 r1,0:76 1:0,A:202919759;C:263054372;G:261102127;T:209748730;N:7784,76,0,,,202919759,263054372,261102127,209748730,7784,SRX4870972,SRS3925953,SRA793500,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.00595,,0.00103,,0.99226,,0.61297,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System