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
28470,SRR26253203,SRX21963295,SRS19039869,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 2,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 22|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND2,Small RNA IFND2,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-2.deadaptor.fq.gz,fastq,278362309.0,11056139.0,IFN4 2.deadaptor.fq.gz,0:25.18,A:71944968;C:54562141;G:73333701;T:78511075;N:10424,25,,,,71944968,54562141,73333701,78511075,10424,SRX21963295,SRS19039869,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.93133,,0.07401,,0.96181,,0.74558,,31,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28471,SRR26253204,SRX21963294,SRS19039868,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 21|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND1,Small RNA IFND1,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-1.deadaptor.fq.gz,fastq,289362334.0,11048590.0,IFN4 1.deadaptor.fq.gz,0:26.19,A:73933649;C:59386039;G:76847534;T:79184583;N:10529,26,,,,73933649,59386039,76847534,79184583,10529,SRX21963294,SRS19039868,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.91683,,0.07099,,0.96132,,0.64882,,25,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28472,SRR26253205,SRX21963293,SRS19039867,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 4,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 20|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA4,Small RNA IFNA4,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-4.deadaptor.fq.gz,fastq,270529395.0,11070360.0,IFN1 4.deadaptor.fq.gz,0:24.44,A:69759888;C:54924667;G:71358091;T:74470720;N:16029,24,,,,69759888,54924667,71358091,74470720,16029,SRX21963293,SRS19039867,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.88469,,0.06696,,0.96664,,0.74853,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28473,SRR26253206,SRX21963292,SRS19039866,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 3,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 19|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA3,Small RNA IFNA3,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-3.deadaptor.fq.gz,fastq,353291957.0,11740560.0,IFN1 3.deadaptor.fq.gz,0:30.09,A:89026549;C:76490337;G:94719420;T:93036955;N:18696,30,,,,89026549,76490337,94719420,93036955,18696,SRX21963292,SRS19039866,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.83151,,0.07199,,0.96471,,0.71641,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28474,SRR26253207,SRX21963291,SRS19039865,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 2,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 18|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA2,Small RNA IFNA2,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-2.deadaptor.fq.gz,fastq,257949577.0,11213774.0,IFN1 2.deadaptor.fq.gz,0:23.00,A:67371681;C:51128621;G:67605590;T:71826657;N:17028,23,,,,67371681,51128621,67605590,71826657,17028,SRX21963291,SRS19039865,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.91396,,0.06536,,0.97197,,0.76269,,23,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28475,SRR26253208,SRX21963290,SRS19039864,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 17|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA1,Small RNA IFNA1,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-1.deadaptor.fq.gz,fastq,329358383.0,11799176.0,IFN1 1.deadaptor.fq.gz,0:27.91,A:84093681;C:68961271;G:86502739;T:89779605;N:21087,27,,,,84093681,68961271,86502739,89779605,21087,SRX21963290,SRS19039864,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.92116,,0.07483,,0.96796,,0.75179,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28476,SRR26253209,SRX21963289,SRS19039863,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 4,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 16|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C4,Small RNA C4,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-4.deadaptor.fq.gz,fastq,251577736.0,10951659.0,Control 4.deadaptor.fq.gz,0:22.97,A:65382449;C:50041232;G:66038625;T:70106464;N:8966,22,,,,65382449,50041232,66038625,70106464,8966,SRX21963289,SRS19039863,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.89744,,0.06821,,0.96607,,0.63829,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28477,SRR26253210,SRX21963288,SRS19039862,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 3,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 15|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C3,Small RNA C3,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-3.deadaptor.fq.gz,fastq,252164979.0,11004167.0,Control 3.deadaptor.fq.gz,0:22.92,A:65850899;C:48466665;G:66708038;T:71130786;N:8591,22,,,,65850899,48466665,66708038,71130786,8591,SRX21963288,SRS19039862,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.91567,,0.06804,,0.96278,,0.75579,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28478,SRR26253211,SRX21963287,SRS19039861,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 4,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 24|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND4,Small RNA IFND4,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-4.deadaptor.fq.gz,fastq,291708053.0,11503883.0,IFN4 4.deadaptor.fq.gz,0:25.36,A:74079231;C:61368459;G:76898572;T:79351225;N:10566,25,,,,74079231,61368459,76898572,79351225,10566,SRX21963287,SRS19039861,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.88888,,0.0633,,0.97305,,0.74862,,23,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28479,SRR26253212,SRX21963286,SRS19039860,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 3,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 23|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND3,Small RNA IFND3,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-3.deadaptor.fq.gz,fastq,349995495.0,11885662.0,IFN4 3.deadaptor.fq.gz,0:29.45,A:87443709;C:76373108;G:92741296;T:93425866;N:11516,29,,,,87443709,76373108,92741296,93425866,11516,SRX21963286,SRS19039860,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.92619,,0.06843,,0.9709,,0.74977,,73,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28480,SRR26253213,SRX21963285,SRS19039859,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 2,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 14|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C2,Small RNA C2,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-2.deadaptor.fq.gz,fastq,254163676.0,10744164.0,Control 2.deadaptor.fq.gz,0:23.66,A:66003417;C:49309846;G:67463940;T:71377644;N:8829,23,,,,66003417,49309846,67463940,71377644,8829,SRX21963285,SRS19039859,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.93068,,0.06626,,0.96441,,0.7492,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28481,SRR26253214,SRX21963284,SRS19039858,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 13|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C1,Small RNA C1,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-1.deadaptor.fq.gz,fastq,267090429.0,11027241.0,Control 1.deadaptor.fq.gz,0:24.22,A:70162511;C:50705437;G:69872659;T:76339682;N:10140,24,,,,70162511,50705437,69872659,76339682,10140,SRX21963284,SRS19039858,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.93267,,0.07189,,0.96735,,0.75447,,21,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28496,SRR26321412,SRX22029502,SRS19102283,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 1,R27,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R27,R27,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R27.fastq,fastq,23400.0,312.0,R27.fastq,0:75,A:7949;C:4612;G:4730;T:6100;N:9,75,,,,7949,4612,4730,6100,9,SRX22029502,SRS19102283,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89642,,0.06772,,0.99827,,0.75,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28497,SRR26321413,SRX22029501,SRS19102284,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 4,R22,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R22,R22,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R22.fastq,fastq,23400.0,312.0,R22.fastq,0:75,A:7470;C:4460;G:5063;T:6404;N:3,75,,,,7470,4460,5063,6404,3,SRX22029501,SRS19102284,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87073,,0.12167,,0.99801,,0.73157,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28498,SRR26321414,SRX22029500,SRS19102281,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R21,R21,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R21,R21,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R21.fastq,fastq,23400.0,312.0,R21.fastq,0:75,A:7540;C:4349;G:4857;T:6646;N:8,75,,,,7540,4349,4857,6646,8,SRX22029500,SRS19102281,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.8839,,0.04494,,0.99768,,0.72769,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28499,SRR26321415,SRX22029499,SRS19102282,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 2,R18,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R18,R18,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R18.fastq,fastq,23400.0,312.0,R18.fastq,0:75,A:7380;C:4430;G:5069;T:6518;N:3,75,,,,7380,4430,5069,6518,3,SRX22029499,SRS19102282,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.11196,,0.99784,,0.69791,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28500,SRR26321416,SRX22029498,SRS19102280,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 1,R17,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R17,R17,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R17.fastq,fastq,23400.0,312.0,R17.fastq,0:75,A:7322;C:4455;G:5111;T:6507;N:5,75,,,,7322,4455,5111,6507,5,SRX22029498,SRS19102280,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90439,,0.12749,,0.99813,,0.71052,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28501,SRR26321417,SRX22029497,SRS19102279,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 5,R1,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R1,R1,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R1.fastq,fastq,23400.0,312.0,R1.fastq,0:75,A:7934;C:4560;G:4922;T:5980;N:4,75,,,,7934,4560,4922,5980,4,SRX22029497,SRS19102279,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87045,,0.10526,,0.99805,,0.71978,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28502,SRR26321418,SRX22029496,SRS19102277,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 4,R64,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R64,R64,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R64.fastq,fastq,23400.0,312.0,R64.fastq,0:75,A:7844;C:4626;G:4804;T:6126;N:0,75,,,,7844,4626,4804,6126,0,SRX22029496,SRS19102277,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90119,,0.07509,,0.99839,,0.8,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28503,SRR26321419,SRX22029495,SRS19102278,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 3,R61,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R61,R61,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R61.fastq,fastq,23400.0,312.0,R61.fastq,0:75,A:7454;C:4556;G:4960;T:6425;N:5,75,,,,7454,4556,4960,6425,5,SRX22029495,SRS19102278,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89098,,0.06015,,0.99813,,0.77102,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28504,SRR26321420,SRX22029494,SRS19102276,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 4,30,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,30,30,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,30.fastq,fastq,23400.0,312.0,30.fastq,0:75,A:7732;C:4528;G:5150;T:5987;N:3,75,,,,7732,4528,5150,5987,3,SRX22029494,SRS19102276,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.88447,,0.13147,,0.99772,,0.71584,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28505,SRR26321421,SRX22029493,SRS19102275,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R11,R11,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R11,R11,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R11.fastq,fastq,23400.0,312.0,R11.fastq,0:75,A:7818;C:4507;G:5107;T:5956;N:12,75,,,,7818,4507,5107,5956,12,SRX22029493,SRS19102275,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89345,,0.11475,,0.99847,,0.82258,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28506,SRR26321422,SRX22029492,SRS19102274,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 2,31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,31,31,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,31.fastq,fastq,23400.0,312.0,31.fastq,0:75,A:7470;C:4619;G:4802;T:6504;N:5,75,,,,7470,4619,4802,6504,5,SRX22029492,SRS19102274,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87699,,0.11111,,0.99829,,0.78918,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28507,SRR26321423,SRX22029491,SRS19102273,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 1,R9,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R9,R9,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R9.fastq,fastq,23400.0,312.0,R9.fastq,0:75,A:8130;C:4537;G:4809;T:5917;N:7,75,,,,8130,4537,4809,5917,7,SRX22029491,SRS19102273,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.83588,,0.05725,,0.99801,,0.68586,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28508,SRR26321424,SRX22029490,SRS19102272,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 4,R33,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R33,R33,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R33.fastq,fastq,23400.0,312.0,R33.fastq,0:75,A:7745;C:4421;G:4867;T:6360;N:7,75,,,,7745,4421,4867,6360,7,SRX22029490,SRS19102272,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.07335,,0.99805,,0.71428,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28509,SRR26321425,SRX22029489,SRS19102271,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 3,R31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R31,R31,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R31.fastq,fastq,23400.0,312.0,R31.fastq,0:75,A:7441;C:4483;G:5163;T:6313;N:0,75,,,,7441,4483,5163,6313,0,SRX22029489,SRS19102271,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.9,,0.05925,,0.9977,,0.68325,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28510,SRR26321426,SRX22029488,SRS19102270,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 2,R29,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R29,R29,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R29.fastq,fastq,23400.0,312.0,R29.fastq,0:75,A:7379;C:4698;G:5166;T:6156;N:1,75,,,,7379,4698,5166,6156,1,SRX22029488,SRS19102270,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91016,,0.05859,,0.99797,,0.74528,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28511,SRR26321427,SRX22029487,SRS19102269,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 2,R62,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R62,R62,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R62.fastq,fastq,23400.0,312.0,R62.fastq,0:75,A:7383;C:4566;G:4713;T:6728;N:10,75,,,,7383,4566,4713,6728,10,SRX22029487,SRS19102269,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91571,,0.05363,,0.99835,,0.77674,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28512,SRR26321428,SRX22029486,SRS19102268,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,Replicate 1 for SHAM,SHAM 1,R63,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R63,R63,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R63.fastq,fastq,23400.0,312.0,R63.fastq,0:75,A:7516;C:4606;G:4765;T:6508;N:5,75,,,,7516,4606,4765,6508,5,SRX22029486,SRS19102268,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90385,,0.0423,,0.99805,,0.72429,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
38290,SRR1731762,SRX821156,SRS800969,SRP051449,PRJNA266270,Danio rerio Transcriptome or Gene expression,PRJNA266270,Other,To identify molecular signals that initiate liver regeneration post 1/3 PH,,,,,Transcriptome during early stage of liver regeneration post 1/3 PH,,breed:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic characterization of zebrafish liver regeneration post 1/3 partial hepatectomy,D.rereios liver regeneration sequencing project,1,1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>,SRP051449,,,6h_run1_R1.fastq.gz 6h_run1_R2.fastq.gz,fastq fastq,2014108128.0,13986862.0,6h,0:72 1:72,A:542840697;C:473739345;G:521450086;T:473979205;N:2098795,72,72,,,542840697,473739345,521450086,473979205,2098795,SRX821156,SRS800969,SRA220726,"Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con",Chinese Academy of Sciences,2,0.92698,0.90124,0.02898,0.0276,0.85141,0.85064,0.41793,0.40779,72,72,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-02-10,Adult,Adult,Liver,Liver and Biliary System
38291,SRR1735290,SRX824451,SRS804070,SRP051556,PRJNA266272,Danio rerio Transcriptome or Gene expression,PRJNA266272,Other,To investigate the mechanism of gene expression profiles and the post transcriptional regulations during liver regeneration post 1/9 PH,,,,,transcriptome during liver regeneration post 1/9 PH,,breed:AB line|strain:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic characterization of zebrafish liver regeneration post 1/9 partial hepatectomy,D.rerios liver regeneration post 1/9 PH sequencing project,1,1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>,SRP051556,,,24h3_R1.fastq.gz 24h3_R2.fastq.gz,fastq fastq,1569651120.0,10900355.0,24h3,0:72 1:72,A:423126744;C:367185056;G:396200408;T:381254240;N:1884672,72,72,,,423126744,367185056,396200408,381254240,1884672,SRX824451,SRS804070,SRA221177,"Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con",Chinese Academy of Sciences,2,0.93264,0.91624,0.03854,0.0375,0.81708,0.81554,0.43719,0.43414,72,72,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-02-10,Adult,Adult,Liver,Liver and Biliary System
38292,SRR1735297,SRX824451,SRS804070,SRP051556,PRJNA266272,Danio rerio Transcriptome or Gene expression,PRJNA266272,Other,To investigate the mechanism of gene expression profiles and the post transcriptional regulations during liver regeneration post 1/9 PH,,,,,transcriptome during liver regeneration post 1/9 PH,,breed:AB line|strain:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic characterization of zebrafish liver regeneration post 1/9 partial hepatectomy,D.rerios liver regeneration post 1/9 PH sequencing project,1,1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>,SRP051556,,,168h1_R1.fastq.gz 168h1_R2.fastq.gz,fastq fastq,2340104400.0,16250725.0,168h1,0:72 1:72,A:667910990;C:526343343;G:603352668;T:540093539;N:2403860,72,72,,,667910990,526343343,603352668,540093539,2403860,SRX824451,SRS804070,SRA221177,"Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con",Chinese Academy of Sciences,2,0.9275,0.90676,0.03565,0.03486,0.85456,0.85421,0.42251,0.42133,72,72,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-02-10,Adult,Adult,Liver,Liver and Biliary 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
52216,SRR9164636,SRX5937422,SRS4850458,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,wt +/+ 3dpf 3,wt +/+ 3dpf 3,,filename:L1700046 Probe 20 plus plus 3dpf 1 2.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,wt +/+ 3dpf 3,wt +/+ 3dpf 3,wt +/+ 3dpf 3,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700046_Probe_20_plus_plus_3dpf_1_2.fq.gz,fastq,2506233674.0,16597574.0,L1700046 Probe 20 plus plus 3dpf 1 2.fq.gz,0:151 1:0,A:634000443;C:604069545;G:613398240;T:654463196;N:302250,151,0,,,634000443,604069545,613398240,654463196,302250,SRX5937422,SRS4850458,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.96178,,0.07984,,0.72125,,0.48053,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52217,SRR9164637,SRX5937421,SRS4850457,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,wt +/+ 3dpf 2,wt +/+ 3dpf 2,,filename:L1700052 Probe 14 plus plus 3dpf 4.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,wt +/+ 3dpf 2,wt +/+ 3dpf 2,wt +/+ 3dpf 2,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700052_Probe_14_plus_plus_3dpf_4.fq.gz,fastq,2552457794.0,16903694.0,L1700052 Probe 14 plus plus 3dpf 4.fq.gz,0:151 1:0,A:645631711;C:614227022;G:612129428;T:680168081;N:301552,151,0,,,645631711,614227022,612129428,680168081,301552,SRX5937421,SRS4850457,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.96269,,0.07747,,0.71871,,0.48604,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52218,SRR9164638,SRX5937420,SRS4850456,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,fgf3t24152  /  7dpf 2,fgf3t24152  /  7dpf 2,,filename:L1700048 Probe 22 minus minus 7dpf 4 5.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,fgf3t24152  /  7dpf 2,fgf3t24152  /  7dpf 2,fgf3t24152  /  7dpf 2,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700048_Probe_22_minus_minus_7dpf_4_5.fq.gz,fastq,2516535951.0,16665801.0,L1700048 Probe 22 minus minus 7dpf 4 5.fq.gz,0:151 1:0,A:660865986;C:587075382;G:595275252;T:673011628;N:307703,151,0,,,660865986,587075382,595275252,673011628,307703,SRX5937420,SRS4850456,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.9567,,0.10788,,0.7134,,0.51087,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52219,SRR9164639,SRX5937419,SRS4850455,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,fgf3t24152  /  7dpf 1,fgf3t24152  /  7dpf 1,,filename:L1700047 Probe 21 minus minus 7dpf 1 2.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,fgf3t24152  /  7dpf 1,fgf3t24152  /  7dpf 1,fgf3t24152  /  7dpf 1,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700047_Probe_21_minus_minus_7dpf_1_2.fq.gz,fastq,2466014673.0,16331223.0,L1700047 Probe 21 minus minus 7dpf 1 2.fq.gz,0:151 1:0,A:625570716;C:591147110;G:589476430;T:659526551;N:293866,151,0,,,625570716,591147110,589476430,659526551,293866,SRX5937419,SRS4850455,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.95779,,0.09881,,0.71206,,0.49427,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52220,SRR9164640,SRX5937418,SRS4850454,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,fgf3t24152  /  3dpf 2,fgf3t24152  /  3dpf 2,,filename:L1700045 Probe 19 minus minus 3dpf 3 4 5.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,fgf3t24152  /  3dpf 2,fgf3t24152  /  3dpf 2,fgf3t24152  /  3dpf 2,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700045_Probe_19_minus_minus_3dpf_3_4_5.fq.gz,fastq,2409258605.0,15955355.0,L1700045 Probe 19 minus minus 3dpf 3 4 5.fq.gz,0:151 1:0,A:608760544;C:578294028;G:574909172;T:647001344;N:293517,151,0,,,608760544,578294028,574909172,647001344,293517,SRX5937418,SRS4850454,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.96392,,0.07974,,0.71467,,0.47801,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52221,SRR9164641,SRX5937417,SRS4850453,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,fgf3t24152  /  3dpf 1,fgf3t24152  /  3dpf 1,,filename:L1700044 Probe 1 minus minus 3dpf 1.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,fgf3t24152  /  3dpf 1,fgf3t24152  /  3dpf 1,fgf3t24152  /  3dpf 1,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700044_Probe_1_minus_minus_3dpf_1.fq.gz,fastq,2424787596.0,16058196.0,L1700044 Probe 1 minus minus 3dpf 1.fq.gz,0:151 1:0,A:605667403;C:588658821;G:580998119;T:649175582;N:287671,151,0,,,605667403,588658821,580998119,649175582,287671,SRX5937417,SRS4850453,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.96678,,0.07043,,0.72151,,0.4886,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52222,SRR9164642,SRX5937416,SRS4850452,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,wt +/+ 7dpf 3,wt +/+ 7dpf 3,,filename:L1700055 Probe 16 plus plus 7dpf 4.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,wt +/+ 7dpf 3,wt +/+ 7dpf 3,wt +/+ 7dpf 3,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700055_Probe_16_plus_plus_7dpf_4.fq.gz,fastq,2406426147.0,15936597.0,L1700055 Probe 16 plus plus 7dpf 4.fq.gz,0:151 1:0,A:621628027;C:570510169;G:570560525;T:643440348;N:287078,151,0,,,621628027,570510169,570560525,643440348,287078,SRX5937416,SRS4850452,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.95873,,0.09322,,0.70849,,0.50116,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52223,SRR9164643,SRX5937415,SRS4850451,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,wt +/+ 7dpf 2,wt +/+ 7dpf 2,,filename:L1700054 Probe 11 plus plus 7dpf 2.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,wt +/+ 7dpf 2,wt +/+ 7dpf 2,wt +/+ 7dpf 2,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700054_Probe_11_plus_plus_7dpf_2.fq.gz,fastq,2388621586.0,15818686.0,L1700054 Probe 11 plus plus 7dpf 2.fq.gz,0:151 1:0,A:604867119;C:572969413;G:574552382;T:635946570;N:286102,151,0,,,604867119,572969413,574552382,635946570,286102,SRX5937415,SRS4850451,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.9601,,0.08858,,0.71226,,0.4818,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52224,SRR9164644,SRX5937414,SRS4850450,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,wt +/+ 3dpf 1,wt +/+ 3dpf 1,,filename:L1700051 Probe 6 plus plus 3dpf 3.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,wt +/+ 3dpf 1,wt +/+ 3dpf 1,wt +/+ 3dpf 1,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700051_Probe_6_plus_plus_3dpf_3.fq.gz,fastq,2516841877.0,16667827.0,L1700051 Probe 6 plus plus 3dpf 3.fq.gz,0:151 1:0,A:638504042;C:602279329;G:599178016;T:676575909;N:304581,151,0,,,638504042,602279329,599178016,676575909,304581,SRX5937414,SRS4850450,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.96561,,0.07463,,0.72054,,0.48315,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52225,SRR9164645,SRX5937413,SRS4850449,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,wt +/+ 7dpf 1,wt +/+ 7dpf 1,,filename:L1700049 Probe 23 plus plus 7dpf 1 3.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,wt +/+ 7dpf 1,wt +/+ 7dpf 1,wt +/+ 7dpf 1,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700049_Probe_23_plus_plus_7dpf_1_3.fq.gz,fastq,2811795311.0,18621161.0,L1700049 Probe 23 plus plus 7dpf 1 3.fq.gz,0:151 1:0,A:718804998;C:669270370;G:672469872;T:750915840;N:334231,151,0,,,718804998,669270370,672469872,750915840,334231,SRX5937413,SRS4850449,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.95734,,0.09739,,0.71256,,0.48704,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52226,SRR9164646,SRX5937412,SRS4850448,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,fgf3t24152  /  7dpf 3,fgf3t24152  /  7dpf 3,,filename:L1700053 Probe 9 minus minus 7dpf 3.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,fgf3t24152  /  7dpf 3,fgf3t24152  /  7dpf 3,fgf3t24152  /  7dpf 3,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700053_Probe_9_minus_minus_7dpf_3.fq.gz,fastq,2201563390.0,14579890.0,L1700053 Probe 9 minus minus 7dpf 3.fq.gz,0:151 1:0,A:559541557;C:523434389;G:527775051;T:590547674;N:264719,151,0,,,559541557,523434389,527775051,590547674,264719,SRX5937412,SRS4850448,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.95732,,0.09772,,0.70678,,0.49199,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
52227,SRR9164647,SRX5937411,SRS4850447,SRP199963,PRJNA541414,Danio rerio Raw sequence reads,PRJNA541414,Other,In most vertebrates  including zebrafish  the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons  little is known about the development and function of thesecells. Here  we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further  expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus  and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover  our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function  suggesting activation of a self compensatory mechanism. Together  these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.,,,,fgf3t24152  /  3dpf 3,fgf3t24152  /  3dpf 3,,filename:L1700050 Probe 2 minus minus 3dpf 2.fq.gz|strain:Tuebingen|dev stage:embryo|sex:not determined|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,fgf3t24152  /  3dpf 3,fgf3t24152  /  3dpf 3,fgf3t24152  /  3dpf 3,library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP199963,,,L1700050_Probe_2_minus_minus_3dpf_2.fq.gz,fastq,2555431890.0,16923390.0,L1700050 Probe 2 minus minus 3dpf 2.fq.gz,0:151 1:0,A:649509144;C:614610346;G:607297438;T:683712219;N:302743,151,0,,,649509144,614610346,607297438,683712219,302743,SRX5937411,SRS4850447,SRA892447,University of Wuerzburg|Department for Physiological Chemistry,University of Wuerzburg,1,0.96502,,0.07688,,0.72381,,0.4855,,151,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,Germany,2019-05-31,Larval,Larval,Brain,Nervous System
59351,SRR11862874,SRX8413250,SRS6725560,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchE,library 10 batchE stress,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:10SMALL GTTTCG L002 R1 001.fastq.gz|batch:5|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchE,10SMALL GTTTCG L002 R1 001.fastq.gz,10SMALL GTTTCG L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,10SMALL_GTTTCG_L002_R1_001.fastq.gz,fastq,610892898.0,9255953.0,10SMALL GTTTCG L002 R1 001.fastq.gz,0:66,A:131858438;C:155399854;G:158242625;T:165382769;N:9212,66,,,,131858438,155399854,158242625,165382769,9212,SRX8413250,SRS6725560,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.07236,,0.0163,,0.95574,,0.71914,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59352,SRR11862875,SRX8413249,SRS6725559,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchE,library 9 batchE control,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:9SMALL GTGGCC L002 R1 001.fastq.gz|batch:5|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchE,9SMALL GTGGCC L002 R1 001.fastq.gz,9SMALL GTGGCC L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,9SMALL_GTGGCC_L002_R1_001.fastq.gz,fastq,681019152.0,10318472.0,9SMALL GTGGCC L002 R1 001.fastq.gz,0:66,A:145919628;C:180332988;G:185160654;T:169595863;N:10019,66,,,,145919628,180332988,185160654,169595863,10019,SRX8413249,SRS6725559,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.03361,,0.00721,,0.97585,,0.72421,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59353,SRR11862876,SRX8413248,SRS6725558,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchD,library 8 batchD stress,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:8SMALL GTGAAA L002 R1 001.fastq.gz|batch:4|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchD,8SMALL GTGAAA L002 R1 001.fastq.gz,8SMALL GTGAAA L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,8SMALL_GTGAAA_L002_R1_001.fastq.gz,fastq,881814912.0,13360832.0,8SMALL GTGAAA L002 R1 001.fastq.gz,0:66,A:223839245;C:210712788;G:239626812;T:207623100;N:12967,66,,,,223839245,210712788,239626812,207623100,12967,SRX8413248,SRS6725558,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.01456,,0.00285,,0.98685,,0.79954,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59354,SRR11862877,SRX8413247,SRS6725557,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchD,library 7 batchD control,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:7SMALL GTCCGC L002 R1 001.fastq.gz|batch:4|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchD,7SMALL GTCCGC L002 R1 001.fastq.gz,7SMALL GTCCGC L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,7SMALL_GTCCGC_L002_R1_001.fastq.gz,fastq,871937682.0,13211177.0,7SMALL GTCCGC L002 R1 001.fastq.gz,0:66,A:187309754;C:240910478;G:236157154;T:207547961;N:12335,66,,,,187309754,240910478,236157154,207547961,12335,SRX8413247,SRS6725557,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.00388,,0.00062,,0.99622,,0.86525,,66,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59355,SRR11862878,SRX8413246,SRS6725556,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchC,library 6 batchC stress,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:6SMALL GTAGAG L002 R1 001.fastq.gz|batch:3|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchC,6SMALL GTAGAG L002 R1 001.fastq.gz,6SMALL GTAGAG L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,6SMALL_GTAGAG_L002_R1_001.fastq.gz,fastq,588357594.0,8914509.0,6SMALL GTAGAG L002 R1 001.fastq.gz,0:66,A:138378307;C:145942814;G:162208729;T:141818898;N:8846,66,,,,138378307,145942814,162208729,141818898,8846,SRX8413246,SRS6725556,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.02473,,0.00511,,0.98317,,0.76412,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59356,SRR11862879,SRX8413245,SRS6725555,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchC,library 5 batchC control,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:5SMALL CCGTCC L002 R1 001.fastq.gz|batch:3|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchC,5SMALL CCGTCC L002 R1 001.fastq.gz,5SMALL CCGTCC L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,5SMALL_CCGTCC_L002_R1_001.fastq.gz,fastq,724072008.0,10970788.0,5SMALL CCGTCC L002 R1 001.fastq.gz,0:66,A:153195532;C:210035381;G:176169980;T:184660888;N:10227,66,,,,153195532,210035381,176169980,184660888,10227,SRX8413245,SRS6725555,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.02036,,0.00355,,0.98265,,0.71654,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59357,SRR11862880,SRX8413244,SRS6725554,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchB,library 4 batchB stress,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:4SMALL ATGTCA L002 R1 001.fastq.gz|batch:2|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchB,4SMALL ATGTCA L002 R1 001.fastq.gz,4SMALL ATGTCA L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,4SMALL_ATGTCA_L002_R1_001.fastq.gz,fastq,734716818.0,11132073.0,4SMALL ATGTCA L002 R1 001.fastq.gz,0:66,A:176688644;C:183414624;G:192032878;T:182569784;N:10888,66,,,,176688644,183414624,192032878,182569784,10888,SRX8413244,SRS6725554,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.03816,,0.00665,,0.97378,,0.80915,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59358,SRR11862881,SRX8413243,SRS6725553,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchB,library 3 batchB control,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:3SMALL AGTTCC L002 R1 001.fastq.gz|batch:2|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchB,3SMALL AGTTCC L002 R1 001.fastq.gz,3SMALL AGTTCC L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,3SMALL_AGTTCC_L002_R1_001.fastq.gz,fastq,639608178.0,9691033.0,3SMALL AGTTCC L002 R1 001.fastq.gz,0:66,A:141927022;C:169937693;G:166391833;T:161342157;N:9473,66,,,,141927022,169937693,166391833,161342157,9473,SRX8413243,SRS6725553,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.00358,,0.00027,,0.99857,,0.92025,,66,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59359,SRR11862882,SRX8413242,SRS6725552,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchF,library 12 batchF stress,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:12SMALL GAGTGG L002 R1 001.fastq.gz|batch:6|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchF,12SMALL GAGTGG L002 R1 001.fastq.gz,12SMALL GAGTGG L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,12SMALL_GAGTGG_L002_R1_001.fastq.gz,fastq,856789890.0,12981665.0,12SMALL GAGTGG L002 R1 001.fastq.gz,0:66,A:197687950;C:209840385;G:245135169;T:204114009;N:12377,66,,,,197687950,209840385,245135169,204114009,12377,SRX8413242,SRS6725552,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.13729,,0.02049,,0.93752,,0.71536,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59360,SRR11862883,SRX8413241,SRS6725551,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchF,library 11 batchF control,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:11SMALL CGTACG L002 R1 001.fastq.gz|batch:6|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from control adult male batchF,11SMALL CGTACG L002 R1 001.fastq.gz,11SMALL CGTACG L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,11SMALL_CGTACG_L002_R1_001.fastq.gz,fastq,891015576.0,13500236.0,11SMALL CGTACG L002 R1 001.fastq.gz,0:66,A:215219357;C:226988408;G:230348786;T:218445888;N:13137,66,,,,215219357,226988408,230348786,218445888,13137,SRX8413241,SRS6725551,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.10021,,0.02466,,0.95789,,0.65844,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59361,SRR11862884,SRX8413240,SRS6725550,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchA,library 2 batchA stress,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Stress|filename:2SMALL AGTCAA L002 R1 001.fastq.gz|batch:1|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of zebrafish spermatozoa  from stressed adult male batchA,2SMALL AGTCAA L002 R1 001.fastq.gz,2SMALL AGTCAA L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,2SMALL_AGTCAA_L002_R1_001.fastq.gz,fastq,790770684.0,11981374.0,2SMALL AGTCAA L002 R1 001.fastq.gz,0:66,A:198694732;C:195900186;G:206731529;T:189432489;N:11748,66,,,,198694732,195900186,206731529,189432489,11748,SRX8413240,SRS6725550,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.06132,,0.01001,,0.96731,,0.807,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
59362,SRR11862885,SRX8413239,SRS6725549,SRP265077,PRJNA635603,Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs,PRJNA635603,Other,A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.,,,,Small RNA seq of  zebrafish spermatozoa from control adult male batchA,library 1 batchA control,,strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:1SMALL CTTGTA L002 R1 001.fastq.gz|batch:1|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA seq of  zebrafish spermatozoa from control adult male batchA,1SMALL CTTGTA L002 R1 001.fastq.gz,1SMALL CTTGTA L002 R1 001.fastq.gz,Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265077,,,1SMALL_CTTGTA_L002_R1_001.fastq.gz,fastq,796394940.0,12066590.0,1SMALL CTTGTA L002 R1 001.fastq.gz,0:66,A:180861950;C:199407609;G:204723388;T:211390521;N:11472,66,,,,180861950,199407609,204723388,211390521,11472,SRX8413239,SRS6725549,SRA1080712,University of Tartu|Department of Pathophysiology,University of Tartu,1,0.01922,,0.00235,,0.99024,,0.87449,,66,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Estonia,2020-05-28,Adult,Adult,Multi-tissue,Multi-system
64249,SRR14373546,SRX10725858,SRS8815710,SRP318063,PRJNA726592,GH overexpression on gonadal microRNAome profile in zebrafish males,PRJNA726592,Other,Evaluate computationally the kinetic parameters  as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.,,,,gh transgenic 6,GH3,,strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:6|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Danio rerio: adult male gonad,GH3,GH3,NEBNext Small RNA Library Prep Set,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina MiSeq,,SRP318063,,,PoolUFPEL-GH6.fastq,fastq,20104659.0,394209.0,PoolUFPEL GH6.fastq,0:51 1:0,A:4462767;C:4536250;G:6471518;T:4633666;N:458,51,0,,,4462767,4536250,6471518,4633666,458,SRX10725858,SRS8815710,SRA1226279,Universidade Federal de Pelotas|CDTec,Universidade Federal de Pelotas,1,0.80185,,0.21091,,0.91547,,0.57044,,51,,B,,usable mapping rate,illumina,miseq,unknown,random_priming,nebnext,bulk,unknown,unknown,,Brazil,2021-04-30,Adult,Adult,Gonad,Reproductive System
64250,SRR14373547,SRX10725857,SRS8815709,SRP318063,PRJNA726592,GH overexpression on gonadal microRNAome profile in zebrafish males,PRJNA726592,Other,Evaluate computationally the kinetic parameters  as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.,,,,gh transgenic 4,GH2,,strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:5|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Danio rerio: adult male gonad,GH2,GH2,NEBNext Small RNA Library Prep Set,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina MiSeq,,SRP318063,,,PoolUFPEL-GH4.fastq,fastq,136130934.0,2669234.0,PoolUFPEL GH4.fastq,0:51 1:0,A:31505752;C:32606264;G:41632000;T:30383900;N:3018,51,0,,,31505752,32606264,41632000,30383900,3018,SRX10725857,SRS8815709,SRA1226279,Universidade Federal de Pelotas|CDTec,Universidade Federal de Pelotas,1,0.78619,,0.26843,,0.87834,,0.48728,,51,,B,,usable mapping rate,illumina,miseq,unknown,random_priming,nebnext,bulk,unknown,unknown,,Brazil,2021-04-30,Adult,Adult,Gonad,Reproductive System
64251,SRR14373548,SRX10725856,SRS8815708,SRP318063,PRJNA726592,GH overexpression on gonadal microRNAome profile in zebrafish males,PRJNA726592,Other,Evaluate computationally the kinetic parameters  as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.,,,,gh transgenic 3,GH1,,strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Danio rerio: adult male gonad,GH1,GH1,NEBNext Small RNA Library Prep Set,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina MiSeq,,SRP318063,,,PoolUFPEL-GH3.fastq,fastq,364152699.0,7140249.0,PoolUFPEL GH3.fastq,0:51 1:0,A:79211373;C:83789471;G:117772711;T:83370974;N:8170,51,0,,,79211373,83789471,117772711,83370974,8170,SRX10725856,SRS8815708,SRA1226279,Universidade Federal de Pelotas|CDTec,Universidade Federal de Pelotas,1,0.80843,,0.18707,,0.92066,,0.59133,,51,,B,,usable mapping rate,illumina,miseq,unknown,random_priming,nebnext,bulk,unknown,unknown,,Brazil,2021-04-30,Adult,Adult,Gonad,Reproductive System
64252,SRR14373549,SRX10725855,SRS8815707,SRP318063,PRJNA726592,GH overexpression on gonadal microRNAome profile in zebrafish males,PRJNA726592,Other,Evaluate computationally the kinetic parameters  as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.,,,,Non transgenic 5,NT3,,strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Danio rerio: adult male gonad,NT3,NT3,NEBNext Small RNA Library Prep Set,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina MiSeq,,SRP318063,,,PoolUFPEL-NT5.fastq,fastq,234366114.0,4595414.0,PoolUFPEL NT5.fastq,0:51 1:0,A:58011123;C:51898677;G:69581397;T:54869614;N:5303,51,0,,,58011123,51898677,69581397,54869614,5303,SRX10725855,SRS8815707,SRA1226279,Universidade Federal de Pelotas|CDTec,Universidade Federal de Pelotas,1,0.83352,,0.35958,,0.85928,,0.50004,,51,,B,,usable mapping rate,illumina,miseq,unknown,random_priming,nebnext,bulk,unknown,unknown,,Brazil,2021-04-30,Adult,Adult,Gonad,Reproductive System
64253,SRR14373550,SRX10725854,SRS8815706,SRP318063,PRJNA726592,GH overexpression on gonadal microRNAome profile in zebrafish males,PRJNA726592,Other,Evaluate computationally the kinetic parameters  as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.,,,,Non transgenic 3,NT2,,strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Danio rerio: adult male gonad,NT2,NT2,NEBNext Small RNA Library Prep Set,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina MiSeq,,SRP318063,,,PoolUFPEL-NT3.fastq,fastq,147963750.0,2901250.0,PoolUFPEL NT3.fastq,0:51 1:0,A:37528568;C:33498521;G:41979920;T:34953411;N:3330,51,0,,,37528568,33498521,41979920,34953411,3330,SRX10725854,SRS8815706,SRA1226279,Universidade Federal de Pelotas|CDTec,Universidade Federal de Pelotas,1,0.75277,,0.34872,,0.86596,,0.53154,,51,,B,,usable mapping rate,illumina,miseq,unknown,random_priming,nebnext,bulk,unknown,unknown,,Brazil,2021-04-30,Adult,Adult,Gonad,Reproductive System
64254,SRR14373551,SRX10725853,SRS8815705,SRP318063,PRJNA726592,GH overexpression on gonadal microRNAome profile in zebrafish males,PRJNA726592,Other,Evaluate computationally the kinetic parameters  as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.,,,,Non transgenic 1,NT1,,strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Danio rerio: adult male gonad,NT1,NT1,NEBNext Small RNA Library Prep Set,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina MiSeq,,SRP318063,,,PoolUFPEL-NT1.fastq,fastq,218363538.0,4281638.0,PoolUFPEL NT1.fastq,0:51 1:0,A:53115431;C:47639482;G:65248144;T:52355651;N:4830,51,0,,,53115431,47639482,65248144,52355651,4830,SRX10725853,SRS8815705,SRA1226279,Universidade Federal de Pelotas|CDTec,Universidade Federal de Pelotas,1,0.83996,,0.3606,,0.87728,,0.50828,,51,,B,,usable mapping rate,illumina,miseq,unknown,random_priming,nebnext,bulk,unknown,unknown,,Brazil,2021-04-30,Adult,Adult,Gonad,Reproductive System
66086,SRR15900240,SRX12190888,SRS10168725,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM+CH 2,,strain:AB|isolate:CH2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab CH2,tchenlab CH2,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_CH_5.8.IP_R1.fastq.gz EOM_CH_5.8.IP_R2.fastq.gz EOM_CH_5.8.Input_R1.fastq.gz EOM_CH_5.8.Input_R2.fastq.gz,fastq fastq fastq fastq,13391108400.0,44637028.0,EOM CH 5.8.IP R1.fastq.gz,0:150 1:150,A:2721241817;C:3886076819;G:4096587749;T:2611313908;N:75888107,150,150,,,2721241817,3886076819,4096587749,2611313908,75888107,SRX12190888,SRS10168725,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.8442,0.59467,0.17491,0.14724,0.86147,0.89112,0.7593,0.63363,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66087,SRR15900241,SRX12190887,SRS10168724,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM+CH 1,,strain:AB|isolate:CH1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab CH1,tchenlab CH1,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_CH_4.16.IP_R1.fastq.gz EOM_CH_4.16.IP_R2.fastq.gz EOM_CH_4.16.Input_R1.fastq.gz EOM_CH_4.16.Input_R2.fastq.gz,fastq fastq fastq fastq,12428976000.0,41429920.0,EOM CH 4.16.IP R1.fastq.gz,0:150 1:150,A:2486344612;C:3648199763;G:3865825828;T:2365039093;N:63566704,150,150,,,2486344612,3648199763,3865825828,2365039093,63566704,SRX12190887,SRS10168724,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.91763,0.6223,0.18817,0.15102,0.84891,0.87957,0.74757,0.64429,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66088,SRR15900242,SRX12190886,SRS10168723,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM 3,,strain:AB|isolate:T3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab T3,tchenlab T3,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_5.9.IP_R1.fastq.gz EOM_5.9.IP_R2.fastq.gz EOM_5.9.Input_R1.fastq.gz EOM_5.9.Input_R2.fastq.gz,fastq fastq fastq fastq,12301780200.0,41005934.0,EOM 5.9.IP R1.fastq.gz,0:150 1:150,A:2415542475;C:3651603114;G:3847935468;T:2318868176;N:67830967,150,150,,,2415542475,3651603114,3847935468,2318868176,67830967,SRX12190886,SRS10168723,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.87516,0.65874,0.18282,0.16547,0.85561,0.87657,0.72193,0.61862,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66089,SRR15900243,SRX12190885,SRS10168722,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM 2,,strain:AB|isolate:T2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab T2,tchenlab T2,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_5.8.IP_R1.fastq.gz EOM_5.8.IP_R2.fastq.gz EOM_5.8.Input_R1.fastq.gz EOM_5.8.Input_R2.fastq.gz,fastq fastq fastq fastq,12373139700.0,41243799.0,EOM 5.8.IP R1.fastq.gz,0:150 1:150,A:2429212483;C:3679585650;G:3865741937;T:2330164654;N:68434976,150,150,,,2429212483,3679585650,3865741937,2330164654,68434976,SRX12190885,SRS10168722,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.88644,0.67829,0.18408,0.16867,0.84652,0.8704,0.76376,0.64158,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66090,SRR15900244,SRX12190884,SRS10168721,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM 1,,strain:AB|isolate:T1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab T1,tchenlab T1,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_4.16.IP_R1.fastq.gz EOM_4.16.IP_R2.fastq.gz EOM_4.16.Input_R1.fastq.gz EOM_4.16.Input_R2.fastq.gz,fastq fastq fastq fastq,13638730800.0,45462436.0,EOM 4.16.IP R1.fastq.gz,0:150 1:150,A:2673949221;C:4057121296;G:4266457677;T:2562131972;N:79070634,150,150,,,2673949221,4057121296,4266457677,2562131972,79070634,SRX12190884,SRS10168721,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.87634,0.65649,0.18403,0.16375,0.85486,0.87913,0.69253,0.6405,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66091,SRR15900245,SRX12190883,SRS10168720,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,DMSO 3,,strain:AB|isolate:C3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab C3,tchenlab C3,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,DMSO_5.9.IP_R1.fastq.gz DMSO_5.9.IP_R2.fastq.gz DMSO_5.9.Input_R1.fastq.gz DMSO_5.9.Input_R2.fastq.gz,fastq fastq fastq fastq,12477964200.0,41593214.0,DMSO 5.9.IP R1.fastq.gz,0:150 1:150,A:2462053397;C:3697418372;G:3878832850;T:2368512335;N:71147246,150,150,,,2462053397,3697418372,3878832850,2368512335,71147246,SRX12190883,SRS10168720,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.94535,0.75289,0.20051,0.18779,0.84139,0.8646,0.74818,0.65269,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66092,SRR15900246,SRX12190882,SRS10168719,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,DMSO 2,,strain:AB|isolate:C2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab C2,tchenlab C2,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,DMSO_5.8.IP_R1.fastq.gz DMSO_5.8.IP_R2.fastq.gz DMSO_5.8.Input_R1.fastq.gz DMSO_5.8.Input_R2.fastq.gz,fastq fastq fastq fastq,12272849400.0,40909498.0,DMSO 5.8.IP R1.fastq.gz,0:150 1:150,A:2381041881;C:3673513092;G:3850518138;T:2295835815;N:71940474,150,150,,,2381041881,3673513092,3850518138,2295835815,71940474,SRX12190882,SRS10168719,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.88711,0.71046,0.18073,0.17436,0.84654,0.8674,0.76218,0.63257,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66093,SRR15900247,SRX12190881,SRS10168718,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,DMSO 1,,strain:AB|isolate:C1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab C1,tchenlab C1,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,DMSO_4.16.IP_R1.fastq.gz DMSO_4.16.IP_R2.fastq.gz DMSO_4.16.Input_R1.fastq.gz DMSO_4.16.Input_R2.fastq.gz,fastq fastq fastq fastq,12900597000.0,43001990.0,DMSO 4.16.IP R1.fastq.gz,0:150 1:150,A:2517062962;C:3854768074;G:4032734290;T:2426295392;N:69736282,150,150,,,2517062962,3854768074,4032734290,2426295392,69736282,SRX12190881,SRS10168718,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.75605,0.5734,0.16268,0.14503,0.8714,0.89422,0.72976,0.64046,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
76734,SRR25361306,SRX21100653,SRS18369835,SRP450509,PRJNA996758,Transcriptome analysis of Zebrafish testis,PRJNA996758,Other,In summary  this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq  which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.,,,,,Zebrafish 3N 3,,strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of triploid zebrafish: mature testis 3,S06,S06,small RNA Sample Pre Kit,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,HiSeq X Ten,,SRP450509,,,Zebrafish-3N-3.fq,fastq,377566667.0,15350070.0,Zebrafish 3N 3.fq,0:24.60,A:96137966;C:76631652;G:87723617;T:117047567;N:25865,24,,,,96137966,76631652,87723617,117047567,25865,SRX21100653,SRS18369835,SRA1676237,Hunan Normal University|College of Life Sciences,Hunan Normal University,1,0.73654,,0.40118,,0.8564,,0.55134,,20,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2023-07-20,Adult,Adult,Gonad,Reproductive System
76735,SRR25361307,SRX21100652,SRS18369834,SRP450509,PRJNA996758,Transcriptome analysis of Zebrafish testis,PRJNA996758,Other,In summary  this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq  which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.,,,,,Zebrafish 3N 2,,strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of triploid zebrafish: mature testis 2,S05,S05,small RNA Sample Pre Kit,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,HiSeq X Ten,,SRP450509,,,Zebrafish-3N-2.fq,fastq,380484856.0,15447197.0,Zebrafish 3N 2.fq,0:24.63,A:97242128;C:77738745;G:86938175;T:118539773;N:26035,24,,,,97242128,77738745,86938175,118539773,26035,SRX21100652,SRS18369834,SRA1676237,Hunan Normal University|College of Life Sciences,Hunan Normal University,1,0.75732,,0.36733,,0.86003,,0.56474,,30,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2023-07-20,Adult,Adult,Gonad,Reproductive System
76736,SRR25361308,SRX21100651,SRS18369833,SRP450509,PRJNA996758,Transcriptome analysis of Zebrafish testis,PRJNA996758,Other,In summary  this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq  which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.,,,,,Zebrafish 3N 1,,strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of triploid zebrafish: mature testis 1,S04,S04,small RNA Sample Pre Kit,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,HiSeq X Ten,,SRP450509,,,Zebrafish-3N-1.fq,fastq,268097774.0,10780393.0,Zebrafish 3N 1.fq,0:24.87,A:68574209;C:53994512;G:62001426;T:83509528;N:18099,24,,,,68574209,53994512,62001426,83509528,18099,SRX21100651,SRS18369833,SRA1676237,Hunan Normal University|College of Life Sciences,Hunan Normal University,1,0.76185,,0.39184,,0.86038,,0.55005,,27,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2023-07-20,Adult,Adult,Gonad,Reproductive System
76737,SRR25361309,SRX21100650,SRS18369832,SRP450509,PRJNA996758,Transcriptome analysis of Zebrafish testis,PRJNA996758,Other,In summary  this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq  which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.,,,,,Zebrafish 2N 3,,strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of diploid zebrafish: mature testis 3,S03,S03,small RNA Sample Pre Kit,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,HiSeq X Ten,,SRP450509,,,Zebrafish-2N-3.fq,fastq,534146242.0,21237464.0,Zebrafish 2N 3.fq,0:25.15,A:134813196;C:109988603;G:122363487;T:166967106;N:13850,25,,,,134813196,109988603,122363487,166967106,13850,SRX21100650,SRS18369832,SRA1676237,Hunan Normal University|College of Life Sciences,Hunan Normal University,1,0.78557,,0.41489,,0.84682,,0.52155,,26,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2023-07-20,Adult,Adult,Gonad,Reproductive System
76738,SRR25361310,SRX21100649,SRS18369831,SRP450509,PRJNA996758,Transcriptome analysis of Zebrafish testis,PRJNA996758,Other,In summary  this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq  which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.,,,,,Zebrafish 2N 2,,strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of diploid zebrafish: mature testis 2,S02,S02,small RNA Sample Pre Kit,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,HiSeq X Ten,,SRP450509,,,Zebrafish-2N-2.fq,fastq,356097642.0,14145771.0,Zebrafish 2N 2.fq,0:25.17,A:90441485;C:73979402;G:81604410;T:110063163;N:9182,25,,,,90441485,73979402,81604410,110063163,9182,SRX21100649,SRS18369831,SRA1676237,Hunan Normal University|College of Life Sciences,Hunan Normal University,1,0.75286,,0.42266,,0.8561,,0.55388,,25,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2023-07-20,Adult,Adult,Gonad,Reproductive System
76739,SRR25361311,SRX21100648,SRS18369830,SRP450509,PRJNA996758,Transcriptome analysis of Zebrafish testis,PRJNA996758,Other,In summary  this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq  which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.,,,,,Zebrafish 2N 1,,strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of diploid zebrafish: mature testis 1,S01,S01,small RNA Sample Pre Kit,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,HiSeq X Ten,,SRP450509,,,Zebrafish-2N-1.fq,fastq,304073792.0,11993451.0,Zebrafish 2N 1.fq,0:25.35,A:78785751;C:62508430;G:69338558;T:93420600;N:20453,25,,,,78785751,62508430,69338558,93420600,20453,SRX21100648,SRS18369830,SRA1676237,Hunan Normal University|College of Life Sciences,Hunan Normal University,1,0.77026,,0.38872,,0.86032,,0.58206,,23,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2023-07-20,Adult,Adult,Gonad,Reproductive System