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
39671,SRR2043046,SRX1041307,SRS947739,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 200nM  sample3,zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3,HBCD 200nM 3,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 3|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3,Sample  HBCD 200nM 3,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP058729,,,Sample_HBCD_200nM-3.fastq.tar.gz,fastq,549695784.0,16657448.0,Sample  HBCD 200nM 3,0:33,A:120885057;C:120386921;G:146939259;T:161323403;N:161144,33,,,,120885057,120386921,146939259,161323403,161144,SRX1041307,SRS947739,SRA269780,MG,Xiamen University,1,0.13819,,0.03714,,0.94968,,0.52004,,33,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-09-18,Larval,Larval,Whole Organism,All anatomical structures
39672,SRR2043044,SRX1041306,SRS947738,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 200nM  sample2,zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep2,HBCD 200nM 2,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 2|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2,Sample  HBCD 200nM 2,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP058729,,,Sample_HBCD_200nM-2.fastq.tar.gz,fastq,566585217.0,17169249.0,Sample  HBCD 200nM 2,0:33,A:119904892;C:129504656;G:159539041;T:157545273;N:91355,33,,,,119904892,129504656,159539041,157545273,91355,SRX1041306,SRS947738,SRA269780,MG,Xiamen University,1,0.07072,,0.01837,,0.96246,,0.52439,,33,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-05-27,Larval,Larval,Whole Organism,All anatomical structures
39673,SRR2043035,SRX1041305,SRS947737,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 200nM  sample1,zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1,HBCD 200nM 1,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 1|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1,Sample  HBCD 200nM 1,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP058729,,,Sample_HBCD_200nM-1.fastq.tar.gz,fastq,636936228.0,17692673.0,Sample  HBCD 200nM 1,0:36,A:138321201;C:126054708;G:184822056;T:187709777;N:28486,36,,,,138321201,126054708,184822056,187709777,28486,SRX1041305,SRS947737,SRA269780,MG,Xiamen University,1,0.04374,,0.0115,,0.97839,,0.29573,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-09-18,Larval,Larval,Whole Organism,All anatomical structures
39674,SRR2043030,SRX1041276,SRS947712,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 2nM  sample3,zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep3,HBCD 2nM 3,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 3|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3,Sample HBCD 2nM 3,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP058729,,,Sample_HBCD_2nM-3.fastq.tar.gz,fastq,636936228.0,17692673.0,Sample HBCD 2nM 3,0:36,A:138321201;C:126054708;G:184822056;T:187709777;N:28486,36,,,,138321201,126054708,184822056,187709777,28486,SRX1041276,SRS947712,SRA269780,MG,Xiamen University,1,0.04377,,0.01174,,0.97812,,0.30675,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-05-27,Larval,Larval,Whole Organism,All anatomical structures
39675,SRR2042999,SRX1041271,SRS947707,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 2nM  sample2,zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2,HBCD 2nM 2,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 2|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2,Sample HBCD 2nM 2,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP058729,,,Sample_HBCD_2nM-2.fastq.tar.gz,fastq,482176476.0,13393791.0,Sample HBCD 2nM 2,0:36,A:104565872;C:92998014;G:137403437;T:147164823;N:44330,36,,,,104565872,92998014,137403437,147164823,44330,SRX1041271,SRS947707,SRA269780,MG,Xiamen University,1,0.0759,,0.02077,,0.97025,,0.33489,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-09-18,Larval,Larval,Whole Organism,All anatomical structures
39676,SRR2040574,SRX1038901,SRS945650,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 2nM  sample1,zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1,HBCD 2nM 1,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 1|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1,Sample HBCD 2nM 1,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>,SRP058729,,,Sample_HBCD_2nM-1.fastq.tar.gz,fastq,327925620.0,9109045.0,Sample HBCD 2nM 1,0:36,A:71167117;C:63917852;G:94874537;T:97936051;N:30063,36,,,,71167117,63917852,94874537,97936051,30063,SRX1038901,SRS945650,SRA269780,MG,Xiamen University,1,0.06484,,0.01622,,0.97459,,0.35746,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-05-27,Larval,Larval,Whole Organism,All anatomical structures
39677,SRR2040573,SRX1038898,SRS945648,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 0nM  sample3,zebrafish at normal developmental age of 72hpf in the control rep3,control 3,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 3|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the control  rep3,Sample control 3,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</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>,SRP058729,,,Sample_control-3.fastq.tar.gz,fastq,456812301.0,13842797.0,Sample control 3,0:33,A:99424011;C:100923631;G:121758068;T:134398048;N:308543,33,,,,99424011,100923631,121758068,134398048,308543,SRX1038898,SRS945648,SRA269780,MG,Xiamen University,1,0.14866,,0.03878,,0.95079,,0.53781,,33,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-09-18,Larval,Larval,Whole Organism,All anatomical structures
39678,SRR2040572,SRX1038893,SRS945643,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,HBCD 0nM  sample2,zebrafish at normal developmental age of 72hpf in the control rep2,control 2,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 2|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the control  rep2,Sample control 2,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</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>,SRP058729,,,,,451846230.0,13692310.0,Sample control 2,0:33,A:100056403;C:97812076;G:121442936;T:132449348;N:85467,33,,,,100056403,97812076,121442936,132449348,85467,SRX1038893,SRS945643,SRA269780,MG,Xiamen University,1,0.06007,,0.01901,,0.96794,,0.4743,,33,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-05-27,Larval,Larval,Whole Organism,All anatomical structures
39679,SRR2040562,SRX1038887,SRS945623,SRP058729,PRJNA284830,MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane,PRJNA284830,Whole Genome Sequencing,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,,,Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.,zebrafish at normal developmental age of 72hpf in the control rep1,control 1,,breed:zebrafish|strain:Wild type TU strain|age:72 hpf£¨hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 1|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish at normal developmental age of 72hpf in the control  rep1,Sample control 1,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</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>,SRP058729,,,Sample_control-1.fastq.tar.gz,fastq,398024253.0,12061341.0,Sample control 1,0:33,A:90133666;C:86672655;G:103932053;T:117192591;N:93288,33,,,,90133666,86672655,103932053,117192591,93288,SRX1038887,SRS945623,SRA269780,MG,Xiamen University,1,0.08082,,0.02367,,0.96106,,0.52033,,33,,B,,usable mapping rate,illumina,early_illumina,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2015-05-27,Larval,Larval,Whole Organism,All anatomical structures
41244,SRR3953261,SRX1977497,SRS1585138,SRP079896,PRJNA335352,Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment,GSE84845,Transcriptome Analysis,Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.,,pubmed:28072866,,500 μg/l BDE47 treatment miRNA,GSM2252184,,source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf,500 μg/l BDE47 treatment miRNA,Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.,6 dpf larvae,,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:Tuebingen|tissue:whole larvae|age:6 dpf,GSM2252184,GSM2252184: 500 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq,GSM2252184,,1,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2252184,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP079896,,,Sample_500_1_filtered.fastq.gz,fastq,427211416.0,18037304.0,GSM2252184 r1,0:23.68 1:0,A:104654735;C:95575450;G:107353019;T:119612667;N:15545,23,0,,,104654735,95575450,107353019,119612667,15545,SRX1977497,SRS1585138,SRA444471,GEO,Tongji University,1,0.85356,,0.06282,,0.88609,,0.63407,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,China,2016-07-26,Larval,Larval,Whole Organism,All anatomical structures
41245,SRR3953260,SRX1977496,SRS1585141,SRP079896,PRJNA335352,Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment,GSE84845,Transcriptome Analysis,Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.,,pubmed:28072866,,5 μg/l BDE47 treatment miRNA,GSM2252183,,source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf,5 μg/l BDE47 treatment miRNA,Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.,6 dpf larvae,,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:Tuebingen|tissue:whole larvae|age:6 dpf,GSM2252183,GSM2252183: 5 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq,GSM2252183,,1,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2252183,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP079896,,,Sample_5_1_filtered.fastq.gz,fastq,450698842.0,19202408.0,GSM2252183 r1,0:23.47 1:0,A:112159775;C:101086362;G:111723361;T:125713845;N:15499,23,0,,,112159775,101086362,111723361,125713845,15499,SRX1977496,SRS1585141,SRA444471,GEO,Tongji University,1,0.84838,,0.06014,,0.88637,,0.6441,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,China,2016-07-26,Larval,Larval,Whole Organism,All anatomical structures
41246,SRR3953259,SRX1977495,SRS1585136,SRP079896,PRJNA335352,Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment,GSE84845,Transcriptome Analysis,Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.,,pubmed:28072866,,s DMSO vehicle miRNA,GSM2252182,,source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf,s DMSO vehicle miRNA,Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.,6 dpf larvae,,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:Tuebingen|tissue:whole larvae|age:6 dpf,GSM2252182,GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq,GSM2252182,,1,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2252182,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP079896,,,Sample_s_1_filtered.fq.gz,fastq,383701320.0,16988819.0,GSM2252182 r1,0:22.59 1:0,A:97700155;C:85144858;G:93319367;T:107531046;N:5894,22,0,,,97700155,85144858,93319367,107531046,5894,SRX1977495,SRS1585136,SRA444471,GEO,Tongji University,1,0.86023,,0.05501,,0.89534,,0.59715,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,China,2016-07-26,Larval,Larval,Whole Organism,All anatomical structures
41247,SRR3953258,SRX1977494,SRS1585137,SRP079896,PRJNA335352,Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment,GSE84845,Transcriptome Analysis,Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.,,pubmed:28072866,,c Wildtype miRNA,GSM2252181,,source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf,c Wildtype miRNA,Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.,6 dpf larvae,,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:Tuebingen|tissue:whole larvae|age:6 dpf,GSM2252181,GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq,GSM2252181,,1,Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2252181,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP079896,,,Sample_c_1_filtered.fastq.gz,fastq,413922462.0,17365113.0,GSM2252181 r1,0:23.84 1:0,A:102173642;C:93233248;G:103684592;T:114815345;N:15635,23,0,,,102173642,93233248,103684592,114815345,15635,SRX1977494,SRS1585137,SRA444471,GEO,Tongji University,1,0.85083,,0.06831,,0.88152,,0.63274,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,China,2016-07-26,Larval,Larval,Whole Organism,All anatomical structures
41457,SRR4449278,SRX2267734,SRS1758938,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S09 RID0445,,strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S09,S09 RID0445,S09 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_009_rawlib.basecaller.bam,bam,56886794.0,2186951.0,IonXpressRNA 009 rawlib.basecaller.bam,0:26.01,A:15763527;C:12934017;G:13233004;T:14956246;N:0,26,,,,15763527,12934017,13233004,14956246,0,SRX2267734,SRS1758938,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.6501,,0.44849,,0.83465,,0.59625,,26,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-25,Gastrula,Embryo,Whole Organism,All anatomical structures
41458,SRR4449277,SRX2267733,SRS1758937,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S10 RID0445,,strain:ABTL|dev stage:51% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S10,S10 RID0445,S10 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_010_rawlib.basecaller.bam,bam,63108712.0,2361941.0,IonXpressRNA 010 rawlib.basecaller.bam,0:26.72,A:16956361;C:14496251;G:15049416;T:16606684;N:0,26,,,,16956361,14496251,15049416,16606684,0,SRX2267733,SRS1758937,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.64387,,0.42592,,0.81091,,0.58276,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41459,SRR4449276,SRX2267732,SRS1758936,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S07 RID0445,,strain:ABTL|dev stage:47% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S07,S07 RID0445,S07 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_007_rawlib.basecaller.bam,bam,50356775.0,1885340.0,IonXpressRNA 007 rawlib.basecaller.bam,0:26.71,A:13603929;C:11508700;G:12096780;T:13147366;N:0,26,,,,13603929,11508700,12096780,13147366,0,SRX2267732,SRS1758936,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.63582,,0.39586,,0.79839,,0.56846,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41460,SRR4449275,SRX2267731,SRS1758935,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S08 RID0445,,strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S08,S08 RID0445,S08 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_008_rawlib.basecaller.bam,bam,63655011.0,2486240.0,IonXpressRNA 008 rawlib.basecaller.bam,0:25.60,A:17274215;C:14286496;G:15277222;T:16817078;N:0,25,,,,17274215,14286496,15277222,16817078,0,SRX2267731,SRS1758935,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.64165,,0.41617,,0.79931,,0.56754,,34,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41461,SRR4449274,SRX2267730,SRS1758933,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S05 RID0445,,strain:ABTL|dev stage:58% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S05,S05 RID0445,S05 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_005_rawlib.basecaller.bam,bam,36352941.0,1403002.0,IonXpressRNA 005 rawlib.basecaller.bam,0:25.91,A:10088289;C:8176923;G:8667822;T:9419907;N:0,25,,,,10088289,8176923,8667822,9419907,0,SRX2267730,SRS1758933,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.59289,,0.36407,,0.80213,,0.57695,,26,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41462,SRR4449273,SRX2267729,SRS1758934,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S06 RID0445,,strain:ABTL|dev stage:43% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S06,S06 RID0445,S06 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_006_rawlib.basecaller.bam,bam,41157611.0,1592351.0,IonXpressRNA 006 rawlib.basecaller.bam,0:25.85,A:11322629;C:9228187;G:9750979;T:10855816;N:0,25,,,,11322629,9228187,9750979,10855816,0,SRX2267729,SRS1758934,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.63095,,0.40683,,0.8003,,0.56985,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41463,SRR4449272,SRX2267728,SRS1758932,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S03 RID0445,,strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S03,S03 RID0445,S03 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_003_rawlib.basecaller.bam,bam,60356442.0,2057592.0,IonXpressRNA 003 rawlib.basecaller.bam,0:29.33,A:17060096;C:13661341;G:13721228;T:15913777;N:0,29,,,,17060096,13661341,13721228,15913777,0,SRX2267728,SRS1758932,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.73029,,0.49935,,0.8225,,0.56029,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41464,SRR4449271,SRX2267727,SRS1758931,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S04 RID0445,,strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S04,S04 RID0445,S04 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_004_rawlib.basecaller.bam,bam,55705225.0,2055064.0,IonXpressRNA 004 rawlib.basecaller.bam,0:27.11,A:15806355;C:12308008;G:12579212;T:15011650;N:0,27,,,,15806355,12308008,12579212,15011650,0,SRX2267727,SRS1758931,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.70796,,0.49815,,0.81444,,0.54452,,41,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41465,SRR4449270,SRX2267726,SRS1758930,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S01 RID0445,,strain:ABTL|dev stage:50% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S01,S01 RID0445,S01 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_001_rawlib.basecaller.bam,bam,35407241.0,1342552.0,IonXpressRNA 001 rawlib.basecaller.bam,0:26.37,A:9988109;C:7841340;G:8187069;T:9390723;N:0,26,,,,9988109,7841340,8187069,9390723,0,SRX2267726,SRS1758930,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.63621,,0.43661,,0.80992,,0.53899,,31,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41466,SRR4449269,SRX2267725,SRS1758928,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S02 RID0445,,strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S02,S02 RID0445,S02 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_002_rawlib.basecaller.bam,bam,40875445.0,1512601.0,IonXpressRNA 002 rawlib.basecaller.bam,0:27.02,A:11593378;C:9124451;G:9444184;T:10713432;N:0,27,,,,11593378,9124451,9444184,10713432,0,SRX2267725,SRS1758928,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.66621,,0.45417,,0.8127,,0.55033,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41467,SRR4449267,SRX2267724,SRS1758927,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S15 RID0445,,strain:ABTL|dev stage:52% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S15,S15 RID0445,S15 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_015_rawlib.basecaller.bam,bam,58421266.0,2091074.0,IonXpressRNA 015 rawlib.basecaller.bam,0:27.94,A:16715618;C:13019609;G:13014639;T:15671400;N:0,27,,,,16715618,13019609,13014639,15671400,0,SRX2267724,SRS1758927,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.71786,,0.51457,,0.83863,,0.53442,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41468,SRR4449266,SRX2267723,SRS1758929,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S16 RID0445,,strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S16,S16 RID0445,S16 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_016_rawlib.basecaller.bam,bam,55022551.0,2073507.0,IonXpressRNA 016 rawlib.basecaller.bam,0:26.54,A:15319738;C:12288588;G:12653066;T:14761159;N:0,26,,,,15319738,12288588,12653066,14761159,0,SRX2267723,SRS1758929,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.68905,,0.46941,,0.80306,,0.55981,,26,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41469,SRR4449265,SRX2267722,SRS1758926,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S13 RID0445,,strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S13,S13 RID0445,S13 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_013_rawlib.basecaller.bam,bam,49641484.0,2028008.0,IonXpressRNA 013 rawlib.basecaller.bam,0:24.48,A:13840820;C:11016762;G:11715475;T:13068427;N:0,24,,,,13840820,11016762,11715475,13068427,0,SRX2267722,SRS1758926,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.55355,,0.3659,,0.81576,,0.55987,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41470,SRR4449264,SRX2267721,SRS1758925,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S14 RID0445,,strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S14,S14 RID0445,S14 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_014_rawlib.basecaller.bam,bam,52969826.0,2019609.0,IonXpressRNA 014 rawlib.basecaller.bam,0:26.23,A:14762618;C:11847782;G:12164393;T:14195033;N:0,26,,,,14762618,11847782,12164393,14195033,0,SRX2267721,SRS1758925,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.65926,,0.45113,,0.80515,,0.56221,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41471,SRR4449263,SRX2267720,SRS1758923,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S11 RID0445,,strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S11,S11 RID0445,S11 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_011_rawlib.basecaller.bam,bam,54877334.0,2122171.0,IonXpressRNA 011 rawlib.basecaller.bam,0:25.86,A:14884144;C:12539815;G:13173981;T:14279394;N:0,25,,,,14884144,12539815,13173981,14279394,0,SRX2267720,SRS1758923,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.62581,,0.40704,,0.82002,,0.59605,,20,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
41472,SRR4449262,SRX2267719,SRS1758924,SRP092030,PRJNA350377,Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly,PRJNA350377,Transcriptome Analysis,Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly,,,Danio rerio embryo at approx. 50% epiboly,Danio rerio embryo at approx. 50% epiboly,S12 RID0445,,strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,S12,S12 RID0445,S12 RID0445,Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP092030,,,IonXpressRNA_012_rawlib.basecaller.bam,bam,51987914.0,1937451.0,IonXpressRNA 012 rawlib.basecaller.bam,0:26.83,A:14499922;C:11778716;G:11957347;T:13751929;N:0,26,,,,14499922,11778716,11957347,13751929,0,SRX2267719,SRS1758924,SRA486759,"UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB","UNIVERSITY OF AMSTERDAM, SILS",1,0.67286,,0.44698,,0.80919,,0.58291,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2017-11-01,Gastrula,Embryo,Whole Organism,All anatomical structures
59623,SRR11974583,SRX8518005,SRS6815486,SRP266770,PRJNA638603,small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish,GSE152189,Transcriptome Analysis,In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.,,pubmed:33602989,,F1 Gamma2 nmbu sncRNA 3,GSM4605882,,tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents,F1 Gamma2 nmbu sncRNA 3,Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values,Whole embryo,,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,,develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents,GSM4605882,GSM4605882: F1 Gamma2 nmbu sncRNA 3; Danio rerio; miRNA Seq,GSM4605882,,1,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,GEO Accession:GSM4605882,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP266770,,,nmbu_sncRNA_6_raw.fq.gz,fastq,566507200.0,11330144.0,GSM4605882 r1,0:50,A:167677443;C:125843251;G:148647392;T:124217714;N:121400,50,,,,167677443,125843251,148647392,124217714,121400,SRX8518005,SRS6815486,SRA1085407,GEO,"Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences",1,0.75254,,0.48205,,0.84346,,0.59219,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Norway,2020-06-10,Gastrula,Embryo,Whole Organism,All anatomical structures
59624,SRR11974582,SRX8518004,SRS6815485,SRP266770,PRJNA638603,small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish,GSE152189,Transcriptome Analysis,In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.,,pubmed:33602989,,F1 Gamma2 nmbu sncRNA 2,GSM4605881,,tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents,F1 Gamma2 nmbu sncRNA 2,Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values,Whole embryo,,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,,develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents,GSM4605881,GSM4605881: F1 Gamma2 nmbu sncRNA 2; Danio rerio; miRNA Seq,GSM4605881,,1,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,GEO Accession:GSM4605881,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP266770,,,nmbu_sncRNA_5_raw.fq.gz,fastq,579779650.0,11595593.0,GSM4605881 r1,0:50,A:173232869;C:126599907;G:152751070;T:127092652;N:103152,50,,,,173232869,126599907,152751070,127092652,103152,SRX8518004,SRS6815485,SRA1085407,GEO,"Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences",1,0.7644,,0.48211,,0.84583,,0.59288,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Norway,2020-06-10,Gastrula,Embryo,Whole Organism,All anatomical structures
59625,SRR11974581,SRX8518003,SRS6815484,SRP266770,PRJNA638603,small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish,GSE152189,Transcriptome Analysis,In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.,,pubmed:33602989,,F1 Gamma1 nmbu sncRNA 1,GSM4605880,,tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents,F1 Gamma1 nmbu sncRNA 1,Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values,Whole embryo,,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,,develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents,GSM4605880,GSM4605880: F1 Gamma1 nmbu sncRNA 1; Danio rerio; miRNA Seq,GSM4605880,,1,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,GEO Accession:GSM4605880,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP266770,,,nmbu_sncRNA_4_raw.fq.gz,fastq,649357050.0,12987141.0,GSM4605880 r1,0:50,A:191891965;C:145644319;G:171130267;T:140550711;N:139788,50,,,,191891965,145644319,171130267,140550711,139788,SRX8518003,SRS6815484,SRA1085407,GEO,"Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences",1,0.75002,,0.44712,,0.84818,,0.57467,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Norway,2020-06-10,Gastrula,Embryo,Whole Organism,All anatomical structures
59626,SRR11974580,SRX8518002,SRS6815483,SRP266770,PRJNA638603,small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish,GSE152189,Transcriptome Analysis,In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.,,pubmed:33602989,,F1 Control3 nmbu sncRNA 3,GSM4605879,,tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents,F1 Control3 nmbu sncRNA 3,Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values,Whole embryo,,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,,develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents,GSM4605879,GSM4605879: F1 Control3 nmbu sncRNA 3; Danio rerio; miRNA Seq,GSM4605879,,1,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,GEO Accession:GSM4605879,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP266770,,,nmbu_sncRNA_3_raw.fq.gz,fastq,641762600.0,12835252.0,GSM4605879 r1,0:50,A:187476040;C:147628502;G:173061052;T:133488938;N:108068,50,,,,187476040,147628502,173061052,133488938,108068,SRX8518002,SRS6815483,SRA1085407,GEO,"Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences",1,0.68333,,0.36693,,0.8493,,0.57501,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Norway,2020-06-10,Gastrula,Embryo,Whole Organism,All anatomical structures
59627,SRR11974579,SRX8518001,SRS6815482,SRP266770,PRJNA638603,small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish,GSE152189,Transcriptome Analysis,In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.,,pubmed:33602989,,F1 Control2 nmbu sncRNA 2,GSM4605878,,tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents,F1 Control2 nmbu sncRNA 2,Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values,Whole embryo,,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,,develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents,GSM4605878,GSM4605878: F1 Control2 nmbu sncRNA 2; Danio rerio; miRNA Seq,GSM4605878,,1,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,GEO Accession:GSM4605878,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP266770,,,nmbu_sncRNA_2_raw.fq.gz,fastq,531815250.0,10636305.0,GSM4605878 r1,0:50,A:155930702;C:122952623;G:141743533;T:111074299;N:114093,50,,,,155930702,122952623,141743533,111074299,114093,SRX8518001,SRS6815482,SRA1085407,GEO,"Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences",1,0.65896,,0.35164,,0.8453,,0.57438,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Norway,2020-06-10,Gastrula,Embryo,Whole Organism,All anatomical structures
59628,SRR11974578,SRX8518000,SRS6815481,SRP266770,PRJNA638603,small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish,GSE152189,Transcriptome Analysis,In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.,,pubmed:33602989,,F1 Control1 nmbu sncRNA 1,GSM4605877,,tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents,F1 Control1 nmbu sncRNA 1,Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values,Whole embryo,,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,,develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents,GSM4605877,GSM4605877: F1 Control1 nmbu sncRNA 1; Danio rerio; miRNA Seq,GSM4605877,,1,Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®  New England Biolabs® inc  USA from each sample 1 μg of total RNA was used as input material.,GEO Accession:GSM4605877,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP266770,,,nmbu_sncRNA_1_raw.fq.gz,fastq,534855250.0,10697105.0,GSM4605877 r1,0:50,A:156249541;C:120087413;G:145230236;T:113171967;N:116093,50,,,,156249541,120087413,145230236,113171967,116093,SRX8518000,SRS6815481,SRA1085407,GEO,"Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences",1,0.74031,,0.40182,,0.83366,,0.60438,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Norway,2020-06-10,Gastrula,Embryo,Whole Organism,All anatomical structures
60445,SRR12272862,SRX8777892,SRS7048444,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_2_4.fq,fastq,542610936.0,21965958.0,C2 C2 2 4.fq.gz,0:24.70,A:95221617;C:122628624;G:167025611;T:157730855;N:4229,24,,,,95221617,122628624,167025611,157730855,4229,SRX8777892,SRS7048444,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.8119,,0.10745,,0.85717,,0.51338,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60446,SRR12272863,SRX8777891,SRS7048443,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_1_4.fq,fastq,542847476.0,22614181.0,C2 C2 1 4.fq.gz,0:24.00,A:99999101;C:125407906;G:162383758;T:155055099;N:1612,24,,,,99999101,125407906,162383758,155055099,1612,SRX8777891,SRS7048443,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84327,,0.10491,,0.83256,,0.52046,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60447,SRR12272864,SRX8777890,SRS7048442,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_2_4.fq,fastq,570918284.0,22577002.0,C1 C1 2 4.fq.gz,0:25.29,A:100121235;C:130480588;G:178656113;T:161652765;N:7583,25,,,,100121235,130480588,178656113,161652765,7583,SRX8777890,SRS7048442,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.85096,,0.12542,,0.82873,,0.51535,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60448,SRR12272865,SRX8777889,SRS7048441,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_1_4.fq,fastq,545089417.0,22812164.0,C1 C1 1 4.fq.gz,0:23.89,A:99851844;C:125314095;G:166401335;T:153521167;N:976,23,,,,99851844,125314095,166401335,153521167,976,SRX8777889,SRS7048441,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84602,,0.11725,,0.83159,,0.51353,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60449,SRR12272866,SRX8777888,SRS7048440,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_2_4.fq,fastq,527443144.0,23174740.0,C0 C0 2 4.fq.gz,0:22.76,A:102368401;C:120843229;G:151690193;T:152540806;N:515,22,,,,102368401,120843229,151690193,152540806,515,SRX8777888,SRS7048440,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83063,,0.08114,,0.85169,,0.50894,,16,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60450,SRR12272867,SRX8777887,SRS7048439,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_1_4.fq,fastq,511759408.0,22673361.0,C0 C0 1 4.fq.gz,0:22.57,A:100879182;C:120237907;G:142799495;T:147842595;N:229,22,,,,100879182,120237907,142799495,147842595,229,SRX8777887,SRS7048439,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83904,,0.0823,,0.84741,,0.49929,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
70542,SRR19996277,SRX16037367,SRS13717223,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 3 [miRNA Seq],GSM6294388,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294388,GSM6294388: High fat diet   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294388 r1,GSM6294388,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD6_AGAACGCA_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294388 r1,0:76 1:0,A:356587691;C:315255282;G:298515494;T:245619001;N:22532,76,0,,,356587691,315255282,298515494,245619001,22532,SRX16037367,SRS13717223,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.54851,,0.13461,,0.86825,,0.63082,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70543,SRR19996278,SRX16037367,SRS13717223,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 3 [miRNA Seq],GSM6294388,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294388,GSM6294388: High fat diet   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294388 r1,GSM6294388,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD6_AGAACGCA_L001_R1_002.fastq.gz,fastq,112508424.0,1480374.0,GSM6294388 r2,0:76 1:0,A:33065142;C:29043993;G:27540664;T:22855718;N:2907,76,0,,,33065142,29043993,27540664,22855718,2907,SRX16037367,SRS13717223,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.55607,,0.14424,,0.86856,,0.65786,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70544,SRR19996279,SRX16037367,SRS13717223,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 3 [miRNA Seq],GSM6294388,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294388,GSM6294388: High fat diet   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294388 r1,GSM6294388,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD6_AGAACGCA_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294388 r3,0:76 1:0,A:356672501;C:315052549;G:298481239;T:245763880;N:29831,76,0,,,356672501,315052549,298481239,245763880,29831,SRX16037367,SRS13717223,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.55045,,0.13717,,0.86624,,0.63636,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70545,SRR19996280,SRX16037367,SRS13717223,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 3 [miRNA Seq],GSM6294388,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294388,GSM6294388: High fat diet   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294388 r1,GSM6294388,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD6_AGAACGCA_L002_R1_002.fastq.gz,fastq,102490788.0,1348563.0,GSM6294388 r4,0:76 1:0,A:30091848;C:26419434;G:25045256;T:20909065;N:25185,76,0,,,30091848,26419434,25045256,20909065,25185,SRX16037367,SRS13717223,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.55804,,0.14662,,0.87172,,0.65108,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70546,SRR19996281,SRX16037366,SRS13717222,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 2 [miRNA Seq],GSM6294387,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294387,GSM6294387: High fat diet   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294387 r1,GSM6294387,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD5_TTACGGCA_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294387 r1,0:76 1:0,A:356185568;C:317412171;G:296624759;T:245755522;N:21980,76,0,,,356185568,317412171,296624759,245755522,21980,SRX16037366,SRS13717222,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.03308,,0.01021,,0.98683,,0.63053,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70547,SRR19996282,SRX16037366,SRS13717222,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 2 [miRNA Seq],GSM6294387,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294387,GSM6294387: High fat diet   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294387 r1,GSM6294387,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD5_TTACGGCA_L001_R1_002.fastq.gz,fastq,95272840.0,1253590.0,GSM6294387 r2,0:76 1:0,A:27984022;C:24743485;G:23171781;T:19371284;N:2268,76,0,,,27984022,24743485,23171781,19371284,2268,SRX16037366,SRS13717222,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.03532,,0.01151,,0.98689,,0.62615,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70548,SRR19996283,SRX16037366,SRS13717222,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 2 [miRNA Seq],GSM6294387,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294387,GSM6294387: High fat diet   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294387 r1,GSM6294387,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD5_TTACGGCA_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294387 r3,0:76 1:0,A:356307606;C:317122785;G:296627283;T:245913596;N:28730,76,0,,,356307606,317122785,296627283,245913596,28730,SRX16037366,SRS13717222,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.03317,,0.01043,,0.98695,,0.61321,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70549,SRR19996284,SRX16037366,SRS13717222,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 2 [miRNA Seq],GSM6294387,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294387,GSM6294387: High fat diet   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294387 r1,GSM6294387,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD5_TTACGGCA_L002_R1_002.fastq.gz,fastq,81590028.0,1073553.0,GSM6294387 r4,0:76 1:0,A:23941275;C:21160767;G:19806367;T:16659459;N:22160,76,0,,,23941275,21160767,19806367,16659459,22160,SRX16037366,SRS13717222,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.03628,,0.01168,,0.98727,,0.61077,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70550,SRR19996285,SRX16037365,SRS13717221,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 1 [miRNA Seq],GSM6294386,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294386,GSM6294386: High fat diet   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294386 r1,GSM6294386,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD4_GTTCGTTG_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294386 r1,0:76 1:0,A:353927140;C:317362066;G:299615370;T:245072880;N:22544,76,0,,,353927140,317362066,299615370,245072880,22544,SRX16037365,SRS13717221,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.037,,0.01164,,0.98754,,0.60746,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70551,SRR19996286,SRX16037365,SRS13717221,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 1 [miRNA Seq],GSM6294386,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294386,GSM6294386: High fat diet   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294386 r1,GSM6294386,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD4_GTTCGTTG_L001_R1_002.fastq.gz,fastq,99836868.0,1313643.0,GSM6294386 r2,0:76 1:0,A:29129510;C:25927485;G:24526547;T:20250631;N:2695,76,0,,,29129510,25927485,24526547,20250631,2695,SRX16037365,SRS13717221,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.04011,,0.01334,,0.98752,,0.60265,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70552,SRR19996287,SRX16037365,SRS13717221,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 1 [miRNA Seq],GSM6294386,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294386,GSM6294386: High fat diet   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294386 r1,GSM6294386,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD4_GTTCGTTG_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294386 r3,0:76 1:0,A:354019911;C:317095108;G:299593671;T:245261603;N:29707,76,0,,,354019911,317095108,299593671,245261603,29707,SRX16037365,SRS13717221,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.03873,,0.01273,,0.98831,,0.61561,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70553,SRR19996288,SRX16037365,SRS13717221,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,High fat diet  rep 1 [miRNA Seq],GSM6294386,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based|geo loc name:missing|collection date:missing,High fat diet   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:High fat diet egg yolk based,GSM6294386,GSM6294386: High fat diet   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294386 r1,GSM6294386,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,HFD4_GTTCGTTG_L002_R1_002.fastq.gz,fastq,89899564.0,1182889.0,GSM6294386 r4,0:76 1:0,A:26203037;C:23320851;G:22042236;T:18308620;N:24820,76,0,,,26203037,23320851,22042236,18308620,24820,SRX16037365,SRS13717221,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.04092,,0.01402,,0.98806,,0.60312,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70554,SRR19996289,SRX16037364,SRS13717220,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 3 [miRNA Seq],GSM6294385,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294385,GSM6294385: Standard diet  rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294385 r1,GSM6294385,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD3_TTGGACCT_L001_R1_001.fastq.gz,fastq,1112575856.0,14639156.0,GSM6294385 r1,0:76 1:0,A:332460940;C:266146733;G:266385877;T:247560550;N:21756,76,0,,,332460940,266146733,266385877,247560550,21756,SRX16037364,SRS13717220,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.72337,,0.15566,,0.8888,,0.58805,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70555,SRR19996290,SRX16037364,SRS13717220,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 3 [miRNA Seq],GSM6294385,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294385,GSM6294385: Standard diet  rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294385 r1,GSM6294385,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD3_TTGGACCT_L002_R1_001.fastq.gz,fastq,1111477200.0,14624700.0,GSM6294385 r2,0:76 1:0,A:332129850;C:265653100;G:266119260;T:247526586;N:48404,76,0,,,332129850,265653100,266119260,247526586,48404,SRX16037364,SRS13717220,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.72447,,0.15572,,0.88982,,0.58556,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70556,SRR19996291,SRX16037363,SRS13717219,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 2 [miRNA Seq],GSM6294384,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294384,GSM6294384: Standard diet  rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294384 r1,GSM6294384,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD2_GGTAACCT_L001_R1_001.fastq.gz,fastq,1210002612.0,15921087.0,GSM6294384 r1,0:76 1:0,A:361374030;C:291914190;G:290545885;T:266145046;N:23461,76,0,,,361374030,291914190,290545885,266145046,23461,SRX16037363,SRS13717219,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.71177,,0.14924,,0.89043,,0.58098,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70557,SRR19996292,SRX16037363,SRS13717219,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 2 [miRNA Seq],GSM6294384,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294384,GSM6294384: Standard diet  rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294384 r1,GSM6294384,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD2_GGTAACCT_L002_R1_001.fastq.gz,fastq,1206642044.0,15876869.0,GSM6294384 r2,0:76 1:0,A:360354644;C:290902220;G:289666907;T:265666862;N:51411,76,0,,,360354644,290902220,289666907,265666862,51411,SRX16037363,SRS13717219,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.71179,,0.15308,,0.8897,,0.57776,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70558,SRR19996293,SRX16037362,SRS13717218,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 1 [miRNA Seq],GSM6294383,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294383,GSM6294383: Standard diet  rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294383 r1,GSM6294383,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD1_AGCAGCAT_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294383 r1,0:76 1:0,A:358278718;C:301640290;G:294524177;T:261533839;N:22976,76,0,,,358278718,301640290,294524177,261533839,22976,SRX16037362,SRS13717218,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.66937,,0.14739,,0.88097,,0.51927,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70559,SRR19996294,SRX16037362,SRS13717218,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 1 [miRNA Seq],GSM6294383,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294383,GSM6294383: Standard diet  rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294383 r1,GSM6294383,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD1_AGCAGCAT_L001_R1_002.fastq.gz,fastq,54586012.0,718237.0,GSM6294383 r2,0:76 1:0,A:16130521;C:13443091;G:13185560;T:11825759;N:1081,76,0,,,16130521,13443091,13185560,11825759,1081,SRX16037362,SRS13717218,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.66892,,0.15871,,0.88534,,0.61412,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70560,SRR19996295,SRX16037362,SRS13717218,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 1 [miRNA Seq],GSM6294383,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294383,GSM6294383: Standard diet  rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294383 r1,GSM6294383,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD1_AGCAGCAT_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294383 r3,0:76 1:0,A:358332225;C:301373187;G:294493629;T:261770800;N:30159,76,0,,,358332225,301373187,294493629,261770800,30159,SRX16037362,SRS13717218,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.67305,,0.14896,,0.87955,,0.51527,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70561,SRR19996296,SRX16037362,SRS13717218,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Standard diet  rep 1 [miRNA Seq],GSM6294383,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing,Standard diet  rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Standard diet,GSM6294383,GSM6294383: Standard diet  rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294383 r1,GSM6294383,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,SD1_AGCAGCAT_L002_R1_002.fastq.gz,fastq,46352704.0,609904.0,GSM6294383 r4,0:76 1:0,A:13671786;C:11396426;G:11168736;T:10092890;N:22866,76,0,,,13671786,11396426,11168736,10092890,22866,SRX16037362,SRS13717218,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.6573,,0.16018,,0.88738,,0.61033,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70562,SRR19996297,SRX16037361,SRS13717217,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 3 [miRNA Seq],GSM6294382,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294382,GSM6294382: Caffeine   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294382 r1,GSM6294382,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF6_CACACCTT_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294382 r1,0:76 1:0,A:358149827;C:299352419;G:291962283;T:266512000;N:23471,76,0,,,358149827,299352419,291962283,266512000,23471,SRX16037361,SRS13717217,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.70651,,0.15791,,0.89079,,0.54917,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70563,SRR19996298,SRX16037361,SRS13717217,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 3 [miRNA Seq],GSM6294382,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294382,GSM6294382: Caffeine   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294382 r1,GSM6294382,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF6_CACACCTT_L001_R1_002.fastq.gz,fastq,10444452.0,137427.0,GSM6294382 r2,0:76 1:0,A:3086609;C:2549103;G:2505559;T:2302999;N:182,76,0,,,3086609,2549103,2505559,2302999,182,SRX16037361,SRS13717217,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.70845,,0.16994,,0.91074,,0.60367,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70564,SRR19996299,SRX16037361,SRS13717217,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 3 [miRNA Seq],GSM6294382,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294382,GSM6294382: Caffeine   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294382 r1,GSM6294382,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF6_CACACCTT_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294382 r3,0:76 1:0,A:358172939;C:299031653;G:291902032;T:266843451;N:49925,76,0,,,358172939,299031653,291902032,266843451,49925,SRX16037361,SRS13717217,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.70533,,0.15953,,0.8912,,0.54519,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70565,SRR19996300,SRX16037361,SRS13717217,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 3 [miRNA Seq],GSM6294382,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294382,GSM6294382: Caffeine   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294382 r1,GSM6294382,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF6_CACACCTT_L002_R1_002.fastq.gz,fastq,6980752.0,91852.0,GSM6294382 r4,0:76 1:0,A:2052067;C:1710495;G:1669139;T:1546003;N:3048,76,0,,,2052067,1710495,1669139,1546003,3048,SRX16037361,SRS13717217,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.12706,,0.04216,,0.98999,,0.58892,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70566,SRR19996301,SRX16037360,SRS13717216,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 2 [miRNA Seq],GSM6294381,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294381,GSM6294381: Caffeine   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294381 r1,GSM6294381,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF5_AAGGAGCA_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294381 r1,0:76 1:0,A:356770857;C:308561625;G:294726765;T:255920941;N:19812,76,0,,,356770857,308561625,294726765,255920941,19812,SRX16037360,SRS13717216,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.63902,,0.12673,,0.89256,,0.59818,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70567,SRR19996302,SRX16037360,SRS13717216,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 2 [miRNA Seq],GSM6294381,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294381,GSM6294381: Caffeine   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294381 r1,GSM6294381,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF5_AAGGAGCA_L001_R1_002.fastq.gz,fastq,233936284.0,3078109.0,GSM6294381 r2,0:76 1:0,A:68694818;C:59188498;G:56704731;T:49340274;N:7963,76,0,,,68694818,59188498,56704731,49340274,7963,SRX16037360,SRS13717216,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.63525,,0.12754,,0.89438,,0.62285,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70568,SRR19996303,SRX16037360,SRS13717216,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 2 [miRNA Seq],GSM6294381,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294381,GSM6294381: Caffeine   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294381 r1,GSM6294381,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF5_AAGGAGCA_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294381 r3,0:76 1:0,A:356829282;C:308257166;G:294736101;T:256149116;N:28335,76,0,,,356829282,308257166,294736101,256149116,28335,SRX16037360,SRS13717216,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.63525,,0.12709,,0.89339,,0.6142,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70569,SRR19996304,SRX16037360,SRS13717216,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 2 [miRNA Seq],GSM6294381,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294381,GSM6294381: Caffeine   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294381 r1,GSM6294381,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF5_AAGGAGCA_L002_R1_002.fastq.gz,fastq,228552368.0,3007268.0,GSM6294381 r4,0:76 1:0,A:67100141;C:57794491;G:55307071;T:48318549;N:32116,76,0,,,67100141,57794491,55307071,48318549,32116,SRX16037360,SRS13717216,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.63992,,0.12925,,0.89301,,0.61101,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70570,SRR19996305,SRX16037359,SRS13717215,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 1 [miRNA Seq],GSM6294380,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294380,GSM6294380: Caffeine   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294380 r1,GSM6294380,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF4_CGATGACA_L001_R1_001.fastq.gz,fastq,1145764676.0,15075851.0,GSM6294380 r1,0:76 1:0,A:335997898;C:289296213;G:277285072;T:243163111;N:22382,76,0,,,335997898,289296213,277285072,243163111,22382,SRX16037359,SRS13717215,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.09883,,0.02592,,0.98612,,0.56195,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70571,SRR19996306,SRX16037359,SRS13717215,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,Caffeine  rep 1 [miRNA Seq],GSM6294380,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h|geo loc name:missing|collection date:missing,Caffeine   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:Caffeine 100 mg/l  0.5 h,GSM6294380,GSM6294380: Caffeine   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294380 r1,GSM6294380,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,CAF4_CGATGACA_L002_R1_001.fastq.gz,fastq,1141773156.0,15023331.0,GSM6294380 r2,0:76 1:0,A:334817584;C:288055961;G:276287149;T:242562822;N:49640,76,0,,,334817584,288055961,276287149,242562822,49640,SRX16037359,SRS13717215,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.10068,,0.0267,,0.98565,,0.57448,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70572,SRR19996307,SRX16037358,SRS13717214,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 1 [miRNA Seq],GSM6294377,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294377,GSM6294377: No treatment   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294377 r1,GSM6294377,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO1_ACAAGACG_L001_R1_001.fastq.gz,fastq,995158668.0,13094193.0,GSM6294377 r1,0:76 1:0,A:299332028;C:245777478;G:239367231;T:210662924;N:19007,76,0,,,299332028,245777478,239367231,210662924,19007,SRX16037358,SRS13717214,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.68203,,0.13258,,0.88534,,0.55078,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70573,SRR19996308,SRX16037358,SRS13717214,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 1 [miRNA Seq],GSM6294377,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 1 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294377,GSM6294377: No treatment   rep 1 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294377 r1,GSM6294377,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO1_ACAAGACG_L002_R1_001.fastq.gz,fastq,990424628.0,13031903.0,GSM6294377 r2,0:76 1:0,A:297965074;C:244354554;G:238178981;T:209884073;N:41946,76,0,,,297965074,244354554,238178981,209884073,41946,SRX16037358,SRS13717214,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.68109,,0.13351,,0.88682,,0.56457,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70574,SRR19996309,SRX16037357,SRS13717213,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 3 [miRNA Seq],GSM6294379,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294379,GSM6294379: No treatment   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294379 r1,GSM6294379,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO3_CTCGAGAA_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294379 r1,0:76 1:0,A:354690733;C:301856703;G:292596517;T:266833618;N:22429,76,0,,,354690733,301856703,292596517,266833618,22429,SRX16037357,SRS13717213,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.71316,,0.14665,,0.89014,,0.54439,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70575,SRR19996310,SRX16037357,SRS13717213,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 3 [miRNA Seq],GSM6294379,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294379,GSM6294379: No treatment   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294379 r1,GSM6294379,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO3_CTCGAGAA_L001_R1_002.fastq.gz,fastq,53318712.0,701562.0,GSM6294379 r2,0:76 1:0,A:15596489;C:13150587;G:12807312;T:11763025;N:1299,76,0,,,15596489,13150587,12807312,11763025,1299,SRX16037357,SRS13717213,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.70664,,0.15394,,0.89633,,0.60523,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70576,SRR19996311,SRX16037357,SRS13717213,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 3 [miRNA Seq],GSM6294379,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294379,GSM6294379: No treatment   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294379 r1,GSM6294379,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO3_CTCGAGAA_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294379 r3,0:76 1:0,A:354711444;C:301582225;G:292594145;T:267082287;N:29899,76,0,,,354711444,301582225,292594145,267082287,29899,SRX16037357,SRS13717213,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.71459,,0.14882,,0.89191,,0.55909,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70577,SRR19996312,SRX16037357,SRS13717213,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 3 [miRNA Seq],GSM6294379,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 3 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294379,GSM6294379: No treatment   rep 3 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294379 r1,GSM6294379,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO3_CTCGAGAA_L002_R1_002.fastq.gz,fastq,51512648.0,677798.0,GSM6294379 r4,0:76 1:0,A:15033755;C:12682878;G:12349291;T:11421784;N:24940,76,0,,,15033755,12682878,12349291,11421784,24940,SRX16037357,SRS13717213,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.69334,,0.15636,,0.89925,,0.60103,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70578,SRR19996313,SRX16037356,SRS13717212,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 2 [miRNA Seq],GSM6294378,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294378,GSM6294378: No treatment   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294378 r1,GSM6294378,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO2_TGCCTTAC_L001_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294378 r1,0:76 1:0,A:361362028;C:298601745;G:291263609;T:264750111;N:22507,76,0,,,361362028,298601745,291263609,264750111,22507,SRX16037356,SRS13717212,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.10097,,0.03311,,0.98689,,0.5206,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70579,SRR19996314,SRX16037356,SRS13717212,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 2 [miRNA Seq],GSM6294378,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294378,GSM6294378: No treatment   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294378 r1,GSM6294378,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO2_TGCCTTAC_L001_R1_002.fastq.gz,fastq,21988016.0,289316.0,GSM6294378 r2,0:76 1:0,A:6560413;C:5359074;G:5257200;T:4810990;N:339,76,0,,,6560413,5359074,5257200,4810990,339,SRX16037356,SRS13717212,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.10905,,0.03769,,0.98697,,0.43718,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70580,SRR19996315,SRX16037356,SRS13717212,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 2 [miRNA Seq],GSM6294378,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294378,GSM6294378: No treatment   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294378 r1,GSM6294378,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO2_TGCCTTAC_L002_R1_001.fastq.gz,fastq,1216000000.0,16000000.0,GSM6294378 r3,0:76 1:0,A:361415922;C:298295563;G:291250734;T:264997086;N:40695,76,0,,,361415922,298295563,291250734,264997086,40695,SRX16037356,SRS13717212,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.1041,,0.03415,,0.98624,,0.47017,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70581,SRR19996316,SRX16037356,SRS13717212,SRP385069,PRJNA856147,Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq],GSE207549,Transcriptome Analysis,Obesity associates with anxiety disorders in adult humans  rodents and fish  although there is also evidence to the contrary. Moreover  it is unknown if this association is developmentally regulated  and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae  which exhibited greater thigmotaxis  erratic swimming and higher whole body cortisol levels than matched controls  and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls  were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf  one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD]. Both models were optimized and validated  the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO  CAF  SD  HFD]  euthanized by ice cold water and snap frozen in liquid nitrogen.,parent bioproject:PRJNA856140,pubmed:37443828,,No treatment  rep 2 [miRNA Seq],GSM6294378,,source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:N1|geo loc name:missing|collection date:missing,No treatment   rep 2 [miRNA Seq],Processing was by the Technion Genome Center  Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench  which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded  and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files  using the reference   miRbase v.22.1 and the preference   Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean  Log2 Fold change  Fold change  p Value  FDR pvalue  Bonferroni for each miR in each model.,whole larvae 30,anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF]  compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet  [HFD  egg yolk based] until 15 dpf  compared to a standard diet [SD].,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,Kept under 14 h light/10 h dark regimen. Water was pH7 7.7  27.7 28.3 C  490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.,tissue:whole larvae 30|strain:AB strain|treatment:N1,GSM6294378,GSM6294378: No treatment   rep 2 [miRNA Seq]; Danio rerio; miRNA Seq,GSM6294378 r1,GSM6294378,1,Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center  Israel. miRNA seq  including other small RNAs. 75 nucleotide single end runs,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP385069,,,NO2_TGCCTTAC_L002_R1_002.fastq.gz,fastq,19738948.0,259723.0,GSM6294378 r4,0:76 1:0,A:5861484;C:4813766;G:4710205;T:4341949;N:11544,76,0,,,5861484,4813766,4710205,4341949,11544,SRX16037356,SRS13717212,SRA1449581,MIGALGalilee Research Institute,MIGALGalilee Research Institute,1,0.11036,,0.03654,,0.98675,,0.45038,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,size_fractionation,unknown,bulk,unknown,unknown,,Israel,2022-07-06,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72366,SRR22805212,SRX18764981,SRS16199877,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,44,BHbisPhenolF 10uM for ribosome profiling replicate 2,,strain:AB|isolate:44|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,BHbisPhenolF 10uM for ribosome profiling replicate 2,44,44,44,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,BHPF_10uM_for_ribosome_profiling_replicate_2_R1.fastq.gz BHPF_10uM_for_ribosome_profiling_replicate_2_R2.fastq.gz,fastq fastq,14888679600.0,49628932.0,BHbisPhenolF 10uM for ribosome profiling replicate 2 R1.fastq.gz,0:150 1:150,A:2177600650;C:2419699560;G:8025893657;T:2265187698;N:298035,150,150,,,2177600650,2419699560,8025893657,2265187698,298035,SRX18764981,SRS16199877,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.64018,0.0,0.06137,1.0,0.83913,,0.80601,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72367,SRR22805213,SRX18764980,SRS16199875,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,43,BHbisPhenolF 10uM for ribosome profiling replicate 1,,strain:AB|isolate:43|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,BHbisPhenolF 10uM for ribosome profiling replicate 1,43,43,43,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,BHPF_10uM_for_ribosome_profiling_replicate_1_R1.fastq.gz BHPF_10uM_for_ribosome_profiling_replicate_1_R2.fastq.gz,fastq fastq,15098951400.0,50329838.0,BHbisPhenolF 10uM for ribosome profiling replicate 1 R1.fastq.gz,0:150 1:150,A:2096550012;C:2382609157;G:8321980233;T:2297312503;N:499495,150,150,,,2096550012,2382609157,8321980233,2297312503,499495,SRX18764980,SRS16199875,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,4e-05,0.62435,0.0,0.06076,0.99993,0.84279,0.75,0.77804,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72368,SRR22805214,SRX18764979,SRS16199876,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,42,DMSO control for ribosome profiling replicate 2,,strain:AB|isolate:42|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,DMSO control for ribosome profiling replicate 2,42,42,42,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,DMSO_control_for_ribosome_profiling_replicate_2_R1.fastq.gz DMSO_control_for_ribosome_profiling_replicate_2_R2.fastq.gz,fastq fastq,13980558600.0,46601862.0,DMSO control for ribosome profiling replicate 2 R1.fastq.gz,0:150 1:150,A:2002344572;C:2128464587;G:7737629750;T:2111846347;N:273344,150,150,,,2002344572,2128464587,7737629750,2111846347,273344,SRX18764979,SRS16199876,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.5747,0.0,0.04778,1.0,0.85411,,0.72362,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72369,SRR22805215,SRX18764978,SRS16199874,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,41,DMSO control for ribosome profiling replicate 1,,strain:AB|isolate:41|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,DMSO control for ribosome profiling replicate 1,41,41,41,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,DMSO_control_for_ribosome_profiling_replicate_1_R1.fastq.gz DMSO_control_for_ribosome_profiling_replicate_1_R2.fastq.gz,fastq fastq,15802088100.0,52673627.0,DMSO control for ribosome profiling replicate 1 R1.fastq.gz,0:150 1:150,A:2301580863;C:2488100262;G:8575515119;T:2436818717;N:73139,150,150,,,2301580863,2488100262,8575515119,2436818717,73139,SRX18764978,SRS16199874,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.59521,0.0,0.05092,1.0,0.84471,,0.75944,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72375,SRR22805221,SRX18764972,SRS16199868,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,36,36.ythdf2 MO for ribosome profiling replicate 2,,strain:AB|isolate:36|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,36.ythdf2 MO for ribosome profiling replicate 2,36,36,36,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,ythdf2_MO_for_ribosome_profiling_replicate_2_R1.fastq.gz ythdf2_MO_for_ribosome_profiling_replicate_2_R2.fastq.gz,fastq fastq,17815545600.0,59385152.0,ythdf2 MO for ribosome profiling replicate 2 R1.fastq.gz,0:150 1:150,A:2527267522;C:2803112888;G:9669305830;T:2815502488;N:356872,150,150,,,2527267522,2803112888,9669305830,2815502488,356872,SRX18764972,SRS16199868,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.6595,0.0,0.05763,1.0,0.82359,,0.76446,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72376,SRR22805222,SRX18764971,SRS16199867,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,35,35.ythdf2 MO for ribosome profiling replicate 1,,strain:AB|isolate:35|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,35.ythdf2 MO for ribosome profiling replicate 1,35,35,35,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,ythdf2_MO_for_ribosome_profiling_replicate_1_R1.fastq.gz ythdf2_MO_for_ribosome_profiling_replicate_1_R2.fastq.gz,fastq fastq,14133373800.0,47111246.0,ythdf2 MO for ribosome profiling replicate 1 R1.fastq.gz,0:150 1:150,A:2066299382;C:2279837250;G:7718113208;T:2069058663;N:65297,150,150,,,2066299382,2279837250,7718113208,2069058663,65297,SRX18764971,SRS16199867,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.68906,0.0,0.06024,1.0,0.81633,,0.76663,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72377,SRR22805223,SRX18764970,SRS16199866,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,34,34.Control knockdown for ribosome profiling replicate 2,,strain:AB|isolate:34|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,34.Control knockdown for ribosome profiling replicate 2,34,34,34,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,Control_knockdown_for_ribosome_profiling_replicate_2_R1.fastq.gz Control_knockdown_for_ribosome_profiling_replicate_2_R2.fastq.gz,fastq fastq,15570048000.0,51900160.0,Control knockdown for ribosome profiling replicate 2 R1.fastq.gz,0:150 1:150,A:2253659984;C:2507376043;G:8463755127;T:2344938646;N:318200,150,150,,,2253659984,2507376043,8463755127,2344938646,318200,SRX18764970,SRS16199866,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.57539,0.0,0.06254,1.0,0.86989,,0.80447,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures
72378,SRR22805224,SRX18764969,SRS16199865,SRP413700,PRJNA906294,Danio rerio Raw sequence reads,PRJNA906294,Other,Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity,,,,33,33.Control knockdown for ribosome profiling replicate 1,,strain:AB|isolate:33|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal,,,,,,,,,33.Control knockdown for ribosome profiling replicate 1,33,33,33,,,miRNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP413700,,,Control_knockdown_for_ribosome_profiling_replicate_1_R1.fastq.gz Control_knockdown_for_ribosome_profiling_replicate_1_R2.fastq.gz,fastq fastq,21657503400.0,72191678.0,Control knockdown for ribosome profiling replicate 1 R1.fastq.gz,0:150 1:150,A:3052615137;C:3123462026;G:12407511554;T:3073813355;N:101328,150,150,,,3052615137,3123462026,12407511554,3073813355,101328,SRX18764969,SRS16199865,SRA1560952,Zhejiang University|Institute of Genetics,Zhejiang University,2,0.0,0.51073,0.0,0.05546,1.0,0.88162,,0.79972,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-12-19,Hatching,Embryo,Whole Organism,All anatomical structures