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
53033,SRR9674344,SRX6434730,SRS5089289,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,rnpc3 WT 1 [miRNA seq],GSM3938561,,source name:Wildtype siblings of rnpc3 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos,rnpc3 WT 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Wildtype siblings of rnpc3 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938561,GSM3938561: rnpc3 WT 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938561,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938561,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Rpc3_1Ctrl.fastq.gz,fastq,1129597674.0,22148974.0,GSM3938561 r1,0:51,A:255811479;C:280511308;G:313965625;T:279284342;N:24920,51,,,,255811479,280511308,313965625,279284342,24920,SRX6434730,SRS5089289,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00979,,0.00166,,0.99588,,0.63728,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53034,SRR9674343,SRX6434729,SRS5089288,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,smn1 WT 1 [miRNA seq],GSM3938560,,source name:Wildtype siblings of smn1 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,smn1 WT 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Wildtype siblings of smn1 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938560,GSM3938560: smn1 WT 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938560,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938560,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Smn1_1Ctrl.fastq.gz,fastq,1381751976.0,27093176.0,GSM3938560 r1,0:51,A:323091185;C:348663819;G:380517013;T:329446099;N:33860,51,,,,323091185,348663819,380517013,329446099,33860,SRX6434729,SRS5089288,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00712,,0.00142,,0.99642,,0.66315,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53035,SRR9674342,SRX6434728,SRS5089287,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin5 WT 1 [miRNA seq],GSM3938559,,source name:Wildtype siblings of germin5 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin5 WT 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Wildtype siblings of germin5 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938559,GSM3938559: gemin5 WT 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938559,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938559,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Gmn5_1Ctrl.fastq.gz,fastq,1347630171.0,26424121.0,GSM3938559 r1,0:51,A:307019777;C:335315873;G:378259746;T:327002846;N:31929,51,,,,307019777,335315873,378259746,327002846,31929,SRX6434728,SRS5089287,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00723,,0.00127,,0.99582,,0.63934,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53036,SRR9674341,SRX6434727,SRS5089286,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,smn1 hom 3 [miRNA seq],GSM3938558,,source name:Homozygous smn1 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,smn1 hom 3 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous smn1 mutants  repeat 3,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938558,GSM3938558: smn1 hom 3 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938558,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938558,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Smn1_3hom.fastq.gz,fastq,1269172638.0,24885738.0,GSM3938558 r1,0:51,A:290351922;C:320656517;G:354834895;T:303300306;N:28998,51,,,,290351922,320656517,354834895,303300306,28998,SRX6434727,SRS5089286,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.0061,,0.00111,,0.9962,,0.5917,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53037,SRR9674340,SRX6434726,SRS5089285,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,smn1 hom 2 [miRNA seq],GSM3938557,,source name:Homozygous smn1 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,smn1 hom 2 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous smn1 mutants  repeat 2,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938557,GSM3938557: smn1 hom 2 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938557,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938557,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Smn1_2hom.fastq.gz,fastq,1625802786.0,31878486.0,GSM3938557 r1,0:51,A:376836190;C:399950981;G:453572869;T:395403783;N:38963,51,,,,376836190,399950981,453572869,395403783,38963,SRX6434726,SRS5089285,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00609,,0.00111,,0.99638,,0.63347,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53038,SRR9674339,SRX6434725,SRS5089284,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,smn1 hom 1 [miRNA seq],GSM3938556,,source name:Homozygous smn1 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,smn1 hom 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous smn1 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938556,GSM3938556: smn1 hom 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938556,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938556,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Smn1_1hom.fastq.gz,fastq,1553527320.0,30461320.0,GSM3938556 r1,0:51,A:360279409;C:388795394;G:432335873;T:372080058;N:36586,51,,,,360279409,388795394,432335873,372080058,36586,SRX6434725,SRS5089284,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00691,,0.00137,,0.99638,,0.61909,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53039,SRR9674338,SRX6434724,SRS5089283,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin5 hom 3 [miRNA seq],GSM3938555,,source name:Homozygous gemin5 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin5 hom 3 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin5 mutants  repeat 3,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938555,GSM3938555: gemin5 hom 3 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938555,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938555,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Gmn5_3hom.fastq.gz,fastq,1162857936.0,22801136.0,GSM3938555 r1,0:51,A:267576310;C:282684680;G:327841913;T:284728561;N:26472,51,,,,267576310,282684680,327841913,284728561,26472,SRX6434724,SRS5089283,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00597,,0.00114,,0.99618,,0.62386,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53040,SRR9674337,SRX6434723,SRS5089282,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin5 hom 2 [miRNA seq],GSM3938554,,source name:Homozygous gemin5 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin5 hom 2 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin5 mutants  repeat 2,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938554,GSM3938554: gemin5 hom 2 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938554,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938554,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Gmn5_2hom.fastq.gz,fastq,1612392846.0,31615546.0,GSM3938554 r1,0:51,A:360634123;C:389619637;G:457463377;T:404638471;N:37238,51,,,,360634123,389619637,457463377,404638471,37238,SRX6434723,SRS5089282,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00538,,0.00085,,0.99677,,0.62726,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53041,SRR9674336,SRX6434722,SRS5089281,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin5 hom 1 [miRNA seq],GSM3938553,,source name:Homozygous gemin5 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin5 hom 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin5 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938553,GSM3938553: gemin5 hom 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938553,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938553,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_Gmn5_1hom.fastq.gz,fastq,1734523362.0,34010262.0,GSM3938553 r1,0:51,A:400823854;C:428868747;G:484830308;T:419961177;N:39276,51,,,,400823854,428868747,484830308,419961177,39276,SRX6434722,SRS5089281,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.00485,,0.00098,,0.99636,,0.65384,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53042,SRR9674335,SRX6434721,SRS5089280,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin6 hom 3 [miRNA seq],GSM3938552,,source name:Homozygous gemin6 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin6 hom 3 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin6 mutants  repeat 3,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938552,GSM3938552: gemin6 hom 3 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938552,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938552,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_G6_3.fastq.gz,fastq,3450343851.0,67653801.0,GSM3938552 r1,0:51,A:777873635;C:888116741;G:969513398;T:814785464;N:54613,51,,,,777873635,888116741,969513398,814785464,54613,SRX6434721,SRS5089280,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.01435,,0.00222,,0.99486,,0.71333,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53043,SRR9674334,SRX6434720,SRS5089279,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin6 hom 2 [miRNA seq],GSM3938551,,source name:Homozygous gemin6 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin6 hom 2 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin6 mutants  repeat 2,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938551,GSM3938551: gemin6 hom 2 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938551,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938551,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_G6_2.fastq.gz,fastq,1586876781.0,31115231.0,GSM3938551 r1,0:51,A:373921059;C:393906222;G:435371208;T:383652895;N:25397,51,,,,373921059,393906222,435371208,383652895,25397,SRX6434720,SRS5089279,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.01456,,0.00199,,0.99488,,0.65884,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53044,SRR9674333,SRX6434719,SRS5089278,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin6 hom 1 [miRNA seq],GSM3938550,,source name:Homozygous gemin6 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin6 hom 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin6 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938550,GSM3938550: gemin6 hom 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938550,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938550,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_G6_1.fastq.gz,fastq,1632291159.0,32005709.0,GSM3938550 r1,0:51,A:387703621;C:405051941;G:452019824;T:387489473;N:26300,51,,,,387703621,405051941,452019824,387489473,26300,SRX6434719,SRS5089278,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.01378,,0.00168,,0.99482,,0.66266,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53045,SRR9674332,SRX6434718,SRS5089277,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin4 hom 3 [miRNA seq],GSM3938549,,source name:Homozygous gemin4 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin4 hom 3 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin4 mutants  repeat 3,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938549,GSM3938549: gemin4 hom 3 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938549,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938549,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_G4_3.fastq.gz,fastq,1079490837.0,21166487.0,GSM3938549 r1,0:51,A:247548301;C:266526237;G:295997407;T:269401582;N:17310,51,,,,247548301,266526237,295997407,269401582,17310,SRX6434718,SRS5089277,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.01616,,0.00211,,0.99486,,0.65494,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53046,SRR9674331,SRX6434717,SRS5089276,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin4 hom 2 [miRNA seq],GSM3938548,,source name:Homozygous gemin4 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin4 hom 2 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin4 mutants  repeat 2,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938548,GSM3938548: gemin4 hom 2 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938548,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938548,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_G4_2.fastq.gz,fastq,6427925862.0,126037762.0,GSM3938548 r1,0:51,A:1491339645;C:1560095279;G:1804953332;T:1571434430;N:103176,51,,,,1491339645,1560095279,1804953332,1571434430,103176,SRX6434717,SRS5089276,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.01032,,0.00157,,0.99504,,0.70577,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,Whole Organism,All anatomical structures
53047,SRR9674330,SRX6434716,SRS5089275,SRP214428,PRJNA554249,the role of SMN complex in tissue regeneration,GSE134187,Transcriptome Analysis,we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.,,,,gemin4 hom 1 [miRNA seq],GSM3938547,,source name:Homozygous gemin4 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos,gemin4 hom 1 [miRNA seq],"Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or ""hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary"" miRNA abundance is measured by RSEM ""rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output"" for mRNA Seq  ""rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15"" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance",Homozygous gemin4 mutants  repeat 1,,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos,GSM3938547,GSM3938547: gemin4 hom 1 [miRNA seq]; Danio rerio; miRNA Seq,GSM3938547,,1,Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3938547,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP214428,,,mir_G4_1.fastq.gz,fastq,3063591624.0,60070424.0,GSM3938547 r1,0:51,A:710248035;C:750319193;G:848095316;T:754879685;N:49395,51,,,,710248035,750319193,848095316,754879685,49395,SRX6434716,SRS5089275,SRA920248,GEO,"Burgess, NHGRI, NIH",1,0.01137,,0.00151,,0.99527,,0.69096,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,bulk,bulk,,United States,2019-07-12,Larval,Larval,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
63643,SRR13979112,SRX10356673,SRS8474629,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep4,GSM5174052,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174052,GSM5174052: miRNA TiBP rep4; Danio rerio; miRNA Seq,GSM5174052,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174052,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s028-indexRPI28-CAAAAG-52_S28_L001_R1_001.fastq.gz,fastq,910334614.0,9013214.0,GSM5174052 r1,0:101 1:0,A:290447743;C:219962173;G:188092578;T:211816048;N:16072,101,0,,,290447743,219962173,188092578,211816048,16072,SRX10356673,SRS8474629,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00011,,0.0,,0.99967,,0.75,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63644,SRR13979111,SRX10356672,SRS8474628,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep3,GSM5174051,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174051,GSM5174051: miRNA TiBP rep3; Danio rerio; miRNA Seq,GSM5174051,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174051,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s027-indexRPI27-ATTCCT-51_S27_L001_R1_001.fastq.gz,fastq,1206610034.0,11946634.0,GSM5174051 r1,0:101 1:0,A:350061820;C:302802434;G:235521116;T:318199102;N:25562,101,0,,,350061820,302802434,235521116,318199102,25562,SRX10356672,SRS8474628,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99965,,0.79166,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63645,SRR13979110,SRX10356671,SRS8474626,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep2,GSM5174050,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174050,GSM5174050: miRNA TiBP rep2; Danio rerio; miRNA Seq,GSM5174050,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174050,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s026-indexRPI26-ATGAGC-50_S26_L001_R1_001.fastq.gz,fastq,464537279.0,4599379.0,GSM5174050 r1,0:101 1:0,A:139497834;C:112216637;G:99887123;T:112926329;N:9356,101,0,,,139497834,112216637,99887123,112926329,9356,SRX10356671,SRS8474626,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00022,,1e-05,,0.99955,,0.61538,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63646,SRR13979109,SRX10356670,SRS8474627,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep1,GSM5174049,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174049,GSM5174049: miRNA TiBP rep1; Danio rerio; miRNA Seq,GSM5174049,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174049,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s025-indexRPI25-ACTGAT-49_S25_L001_R1_001.fastq.gz,fastq,1146926508.0,11355708.0,GSM5174049 r1,0:101 1:0,A:344954395;C:275566512;G:235491109;T:290891698;N:22794,101,0,,,344954395,275566512,235491109,290891698,22794,SRX10356670,SRS8474627,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,1e-05,,0.99965,,0.71875,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63647,SRR13979108,SRX10356669,SRS8474625,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep4,GSM5174048,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174048,GSM5174048: miRNA TPP rep4; Danio rerio; miRNA Seq,GSM5174048,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174048,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s036-indexRPI36-CCAACA-60_S36_L001_R1_001.fastq.gz,fastq,927517340.0,9183340.0,GSM5174048 r1,0:101 1:0,A:288988916;C:242744912;G:181427113;T:214337769;N:18630,101,0,,,288988916,242744912,181427113,214337769,18630,SRX10356669,SRS8474625,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00023,,1e-05,,0.99955,,0.70731,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63648,SRR13979107,SRX10356668,SRS8474624,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep3,GSM5174047,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174047,GSM5174047: miRNA TPP rep3; Danio rerio; miRNA Seq,GSM5174047,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174047,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s035-indexRPI35-CATTTT-59_S35_L001_R1_001.fastq.gz,fastq,1013252907.0,10032207.0,GSM5174047 r1,0:101 1:0,A:295518831;C:243561888;G:197719671;T:276430583;N:21934,101,0,,,295518831,243561888,197719671,276430583,21934,SRX10356668,SRS8474624,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99973,,0.48,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63649,SRR13979106,SRX10356667,SRS8474623,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep2,GSM5174046,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174046,GSM5174046: miRNA TPP rep2; Danio rerio; miRNA Seq,GSM5174046,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174046,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s034-indexRPI34-CATGGC-58_S34_L001_R1_001.fastq.gz,fastq,907210381.0,8982281.0,GSM5174046 r1,0:101 1:0,A:265012714;C:227793861;G:194928689;T:219454152;N:20965,101,0,,,265012714,227793861,194928689,219454152,20965,SRX10356667,SRS8474623,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99965,,0.875,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63650,SRR13979105,SRX10356666,SRS8474622,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep1,GSM5174045,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174045,GSM5174045: miRNA TPP rep1; Danio rerio; miRNA Seq,GSM5174045,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174045,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s033-indexRPI33-CAGGCG-57_S33_L001_R1_001.fastq.gz,fastq,980681013.0,9709713.0,GSM5174045 r1,0:101 1:0,A:286952877;C:245397809;G:220787030;T:227522023;N:21274,101,0,,,286952877,245397809,220787030,227522023,21274,SRX10356666,SRS8474622,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,1e-05,,0.99961,,0.72222,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63651,SRR13979104,SRX10356665,SRS8474621,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep4,GSM5174044,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174044,GSM5174044: miRNA TBPH rep4; Danio rerio; miRNA Seq,GSM5174044,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174044,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s012-indexRPI12-CTTGTA-24_S12_L001_R1_001.fastq.gz,fastq,879997850.0,8712850.0,GSM5174044 r1,0:101 1:0,A:257202916;C:211754629;G:179803383;T:231218549;N:18373,101,0,,,257202916,211754629,179803383,231218549,18373,SRX10356665,SRS8474621,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00022,,0.0,,0.99961,,0.55,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63652,SRR13979103,SRX10356664,SRS8474620,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep3,GSM5174043,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174043,GSM5174043: miRNA TBPH rep3; Danio rerio; miRNA Seq,GSM5174043,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174043,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s011-indexRPI11-GGCTAC-23_S11_L001_R1_001.fastq.gz,fastq,883707883.0,8749583.0,GSM5174043 r1,0:101 1:0,A:256575313;C:222504855;G:189827000;T:214781797;N:18918,101,0,,,256575313,222504855,189827000,214781797,18918,SRX10356664,SRS8474620,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,0.0,,0.99961,,0.725,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63653,SRR13979102,SRX10356663,SRS8474619,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep2,GSM5174042,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174042,GSM5174042: miRNA TBPH rep2; Danio rerio; miRNA Seq,GSM5174042,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174042,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s010-indexRPI10-TAGCTT-22_S10_L001_R1_001.fastq.gz,fastq,727499667.0,7202967.0,GSM5174042 r1,0:101 1:0,A:212029291;C:175832603;G:148851978;T:190770471;N:15324,101,0,,,212029291,175832603,148851978,190770471,15324,SRX10356663,SRS8474619,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00025,,1e-05,,0.99951,,0.68181,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63654,SRR13979101,SRX10356662,SRS8474618,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep1,GSM5174041,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174041,GSM5174041: miRNA TBPH rep1; Danio rerio; miRNA Seq,GSM5174041,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174041,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s009-indexRPI9-GATCAG-21_S9_L001_R1_001.fastq.gz,fastq,351322743.0,3478443.0,GSM5174041 r1,0:101 1:0,A:105338110;C:85172820;G:75749691;T:85054964;N:7158,101,0,,,105338110,85172820,75749691,85054964,7158,SRX10356662,SRS8474618,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00036,,1e-05,,0.99953,,0.52238,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63655,SRR13979100,SRX10356661,SRS8474616,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep4,GSM5174040,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174040,GSM5174040: miRNA TCEP rep4; Danio rerio; miRNA Seq,GSM5174040,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174040,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s044-indexRPI44-TATAAT-72_S44_L001_R1_001.fastq.gz,fastq,904258656.0,8953056.0,GSM5174040 r1,0:101 1:0,A:282578101;C:207780974;G:175938229;T:237943510;N:17842,101,0,,,282578101,207780974,175938229,237943510,17842,SRX10356661,SRS8474616,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.0002,,0.0,,0.99951,,0.72972,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63656,SRR13979099,SRX10356660,SRS8474615,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep3,GSM5174039,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174039,GSM5174039: miRNA TCEP rep3; Danio rerio; miRNA Seq,GSM5174039,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174039,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s043-indexRPI43-TACAGC-71_S43_L001_R1_001.fastq.gz,fastq,908098777.0,8991077.0,GSM5174039 r1,0:101 1:0,A:274350569;C:227463819;G:185316266;T:220948697;N:19426,101,0,,,274350569,227463819,185316266,220948697,19426,SRX10356660,SRS8474615,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00015,,0.0,,0.99965,,0.57142,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63657,SRR13979098,SRX10356659,SRS8474617,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep2,GSM5174038,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174038,GSM5174038: miRNA TCEP rep2; Danio rerio; miRNA Seq,GSM5174038,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174038,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s042-indexRPI42-TAATCG-70_S42_L001_R1_001.fastq.gz,fastq,738320403.0,7310103.0,GSM5174038 r1,0:101 1:0,A:221107544;C:178181142;G:152128298;T:186889068;N:14351,101,0,,,221107544,178181142,152128298,186889068,14351,SRX10356659,SRS8474617,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00017,,0.0,,0.99965,,0.59375,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63658,SRR13979097,SRX10356658,SRS8474612,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep1,GSM5174037,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174037,GSM5174037: miRNA TCEP rep1; Danio rerio; miRNA Seq,GSM5174037,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174037,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s041-indexRPI41-GACGAC-69_S41_L001_R1_001.fastq.gz,fastq,470221761.0,4655661.0,GSM5174037 r1,0:101 1:0,A:142688200;C:117856681;G:100380615;T:109286679;N:9586,101,0,,,142688200,117856681,100380615,109286679,9586,SRX10356658,SRS8474612,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00028,,1e-05,,0.99951,,0.66666,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63659,SRR13979096,SRX10356657,SRS8474613,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep4,GSM5174036,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174036,GSM5174036: miRNA TDBPP rep4; Danio rerio; miRNA Seq,GSM5174036,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174036,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s024-indexRPI24-GGTAGC-48_S24_L001_R1_001.fastq.gz,fastq,889897668.0,8810868.0,GSM5174036 r1,0:101 1:0,A:253810688;C:216798740;G:203615337;T:215653771;N:19132,101,0,,,253810688,216798740,203615337,215653771,19132,SRX10356657,SRS8474613,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,0.0,,0.99963,,0.41176,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63660,SRR13979095,SRX10356656,SRS8474614,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep3,GSM5174035,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174035,GSM5174035: miRNA TDBPP rep3; Danio rerio; miRNA Seq,GSM5174035,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174035,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s023-indexRPI23-GAGTGG-47_S23_L001_R1_001.fastq.gz,fastq,528666623.0,5234323.0,GSM5174035 r1,0:101 1:0,A:145917522;C:125201606;G:128827845;T:128709318;N:10332,101,0,,,145917522,125201606,128827845,128709318,10332,SRX10356656,SRS8474614,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,0.0,,0.99961,,0.56818,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63661,SRR13979094,SRX10356655,SRS8474609,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep2,GSM5174034,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174034,GSM5174034: miRNA TDBPP rep2; Danio rerio; miRNA Seq,GSM5174034,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174034,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s022-indexRPI22-CGTACG-46_S22_L001_R1_001.fastq.gz,fastq,906963537.0,8979837.0,GSM5174034 r1,0:101 1:0,A:246251307;C:236436405;G:206539134;T:217717657;N:19034,101,0,,,246251307,236436405,206539134,217717657,19034,SRX10356655,SRS8474609,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00015,,0.0,,0.99967,,0.65384,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63662,SRR13979093,SRX10356654,SRS8474611,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep1,GSM5174033,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174033,GSM5174033: miRNA TDBPP rep1; Danio rerio; miRNA Seq,GSM5174033,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174033,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s021-indexRPI21-GTTTCG-45_S21_L001_R1_001.fastq.gz,fastq,556898547.0,5513847.0,GSM5174033 r1,0:101 1:0,A:149304325;C:137357612;G:124103413;T:146121425;N:11772,101,0,,,149304325,137357612,124103413,146121425,11772,SRX10356654,SRS8474611,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,0.0,,0.99957,,0.7027,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63663,SRR13979092,SRX10356653,SRS8474610,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep4,GSM5174032,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174032,GSM5174032: miRNA TCPP rep4; Danio rerio; miRNA Seq,GSM5174032,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174032,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s016-indexRPI16-CCGTCC-28_S16_L001_R1_001.fastq.gz,fastq,885697179.0,8769279.0,GSM5174032 r1,0:101 1:0,A:247836719;C:241737695;G:181087463;T:215012979;N:22323,101,0,,,247836719,241737695,181087463,215012979,22323,SRX10356653,SRS8474610,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,0.0,,0.99967,,0.68571,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63664,SRR13979091,SRX10356652,SRS8474608,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep3,GSM5174031,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174031,GSM5174031: miRNA TCPP rep3; Danio rerio; miRNA Seq,GSM5174031,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174031,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s015-indexRPI15-ATGTCA-27_S15_L001_R1_001.fastq.gz,fastq,566510010.0,5609010.0,GSM5174031 r1,0:101 1:0,A:170383116;C:137048514;G:115945259;T:143122249;N:10872,101,0,,,170383116,137048514,115945259,143122249,10872,SRX10356652,SRS8474608,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00025,,0.0,,0.99967,,0.54347,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63665,SRR13979090,SRX10356651,SRS8474607,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep2,GSM5174030,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174030,GSM5174030: miRNA TCPP rep2; Danio rerio; miRNA Seq,GSM5174030,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174030,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s014-indexRPI14-AGTTCC-26_S14_L001_R1_001.fastq.gz,fastq,892405902.0,8835702.0,GSM5174030 r1,0:101 1:0,A:259754435;C:224608997;G:182748088;T:225275385;N:18997,101,0,,,259754435,224608997,182748088,225275385,18997,SRX10356651,SRS8474607,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00022,,0.0,,0.99951,,0.64285,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63666,SRR13979089,SRX10356650,SRS8474606,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep1,GSM5174029,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174029,GSM5174029: miRNA TCPP rep1; Danio rerio; miRNA Seq,GSM5174029,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174029,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s013-indexRPI13-AGTCAA-25_S13_L001_R1_001.fastq.gz,fastq,1059166295.0,10486795.0,GSM5174029 r1,0:101 1:0,A:329962449;C:255719926;G:216763563;T:256700660;N:19697,101,0,,,329962449,255719926,216763563,256700660,19697,SRX10356650,SRS8474606,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,1e-05,,0.99969,,0.63636,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63667,SRR13979088,SRX10356649,SRS8474605,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep4,GSM5174028,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174028,GSM5174028: miRNA TBBPA rep4; Danio rerio; miRNA Seq,GSM5174028,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174028,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s008-indexRPI8-ACTTGA-20_S8_L001_R1_001.fastq.gz,fastq,868526270.0,8599270.0,GSM5174028 r1,0:101 1:0,A:259616680;C:210636450;G:178110756;T:220145615;N:16769,101,0,,,259616680,210636450,178110756,220145615,16769,SRX10356649,SRS8474605,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00023,,0.0,,0.99961,,0.67441,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63668,SRR13979087,SRX10356648,SRS8474604,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep3,GSM5174027,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174027,GSM5174027: miRNA TBBPA rep3; Danio rerio; miRNA Seq,GSM5174027,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174027,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s007-indexRPI7-CAGATC-19_S7_L001_R1_001.fastq.gz,fastq,493578011.0,4886911.0,GSM5174027 r1,0:101 1:0,A:147046152;C:124953541;G:102431606;T:119137120;N:9592,101,0,,,147046152,124953541,102431606,119137120,9592,SRX10356648,SRS8474604,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,1e-05,,0.99947,,0.76744,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63669,SRR13979086,SRX10356647,SRS8474603,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep2,GSM5174026,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174026,GSM5174026: miRNA TBBPA rep2; Danio rerio; miRNA Seq,GSM5174026,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174026,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s006-indexRPI6-GCCAAT-18_S6_L001_R1_001.fastq.gz,fastq,910368853.0,9013553.0,GSM5174026 r1,0:101 1:0,A:270122236;C:230334670;G:190520709;T:219373774;N:17464,101,0,,,270122236,230334670,190520709,219373774,17464,SRX10356647,SRS8474603,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00023,,0.0,,0.99949,,0.72727,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63670,SRR13979085,SRX10356646,SRS8474602,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep1,GSM5174025,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174025,GSM5174025: miRNA TBBPA rep1; Danio rerio; miRNA Seq,GSM5174025,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174025,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s005-indexRPI5-ACAGTG-17_S5_L001_R1_001.fastq.gz,fastq,894131992.0,8852792.0,GSM5174025 r1,0:101 1:0,A:261443048;C:220215927;G:200185007;T:212270956;N:17054,101,0,,,261443048,220215927,200185007,212270956,17054,SRX10356646,SRS8474602,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,1e-05,,0.99953,,0.7027,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63671,SRR13979084,SRX10356645,SRS8474601,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep4,GSM5174024,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174024,GSM5174024: miRNA TBBPA DBPE rep4; Danio rerio; miRNA Seq,GSM5174024,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174024,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s040-indexRPI40-CTCAGA-68_S40_L001_R1_001.fastq.gz,fastq,567614950.0,5619950.0,GSM5174024 r1,0:101 1:0,A:171789620;C:142600627;G:115292068;T:137921194;N:11441,101,0,,,171789620,142600627,115292068,137921194,11441,SRX10356645,SRS8474601,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00014,,0.0,,0.99965,,0.55555,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63672,SRR13979083,SRX10356644,SRS8474600,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep3,GSM5174023,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174023,GSM5174023: miRNA TBBPA DBPE rep3; Danio rerio; miRNA Seq,GSM5174023,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174023,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s039-indexRPI39-CTATAC-67_S39_L001_R1_001.fastq.gz,fastq,883651020.0,8749020.0,GSM5174023 r1,0:101 1:0,A:267266527;C:221471697;G:172032269;T:222861646;N:18881,101,0,,,267266527,221471697,172032269,222861646,18881,SRX10356644,SRS8474600,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,1e-05,,0.99959,,0.65116,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63673,SRR13979082,SRX10356643,SRS8474599,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep2,GSM5174022,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174022,GSM5174022: miRNA TBBPA DBPE rep2; Danio rerio; miRNA Seq,GSM5174022,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174022,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s038-indexRPI38-CTAGCT-66_S38_L001_R1_001.fastq.gz,fastq,311086666.0,3080066.0,GSM5174022 r1,0:101 1:0,A:90852851;C:77957592;G:63570096;T:78699630;N:6497,101,0,,,90852851,77957592,63570096,78699630,6497,SRX10356643,SRS8474599,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00036,,1e-05,,0.99947,,0.6875,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63674,SRR13979081,SRX10356642,SRS8474598,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep1,GSM5174021,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174021,GSM5174021: miRNA TBBPA DBPE rep1; Danio rerio; miRNA Seq,GSM5174021,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174021,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s037-indexRPI37-CGGAAT-65_S37_L001_R1_001.fastq.gz,fastq,1002314506.0,9923906.0,GSM5174021 r1,0:101 1:0,A:303735625;C:240217618;G:214324562;T:244016797;N:19904,101,0,,,303735625,240217618,214324562,244016797,19904,SRX10356642,SRS8474598,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,1e-05,,0.99953,,0.66666,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63675,SRR13979080,SRX10356641,SRS8474597,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep4,GSM5174020,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174020,GSM5174020: miRNA IPP rep4; Danio rerio; miRNA Seq,GSM5174020,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174020,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s032-indexRPI32-CACTCA-56_S32_L001_R1_001.fastq.gz,fastq,1129258881.0,11180781.0,GSM5174020 r1,0:101 1:0,A:335239774;C:296599595;G:223965990;T:273431685;N:21837,101,0,,,335239774,296599595,223965990,273431685,21837,SRX10356641,SRS8474597,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99959,,0.75,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63676,SRR13979079,SRX10356640,SRS8474596,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep3,GSM5174019,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174019,GSM5174019: miRNA IPP rep3; Danio rerio; miRNA Seq,GSM5174019,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174019,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s031-indexRPI31-CACGAT-55_S31_L001_R1_001.fastq.gz,fastq,1364695941.0,13511841.0,GSM5174019 r1,0:101 1:0,A:408343873;C:341704999;G:281119661;T:333499060;N:28348,101,0,,,408343873,341704999,281119661,333499060,28348,SRX10356640,SRS8474596,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00016,,0.0,,0.99961,,0.68965,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63677,SRR13979078,SRX10356639,SRS8474595,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep2,GSM5174018,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174018,GSM5174018: miRNA IPP rep2; Danio rerio; miRNA Seq,GSM5174018,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174018,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s030-indexRPI30-CACCGG-54_S30_L001_R1_001.fastq.gz,fastq,1118435923.0,11073623.0,GSM5174018 r1,0:101 1:0,A:322914077;C:292720303;G:241919484;T:260855307;N:26752,101,0,,,322914077,292720303,241919484,260855307,26752,SRX10356639,SRS8474595,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.0002,,1e-05,,0.99959,,0.74285,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63678,SRR13979077,SRX10356638,SRS8474594,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep1,GSM5174017,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174017,GSM5174017: miRNA IPP rep1; Danio rerio; miRNA Seq,GSM5174017,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174017,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s029-indexRPI29-CAACTA-53_S29_L001_R1_001.fastq.gz,fastq,965915217.0,9563517.0,GSM5174017 r1,0:101 1:0,A:298517953;C:241792467;G:190277966;T:235308237;N:18594,101,0,,,298517953,241792467,190277966,235308237,18594,SRX10356638,SRS8474594,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00011,,0.0,,0.99973,,0.55,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63679,SRR13979076,SRX10356637,SRS8474593,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep4,GSM5174016,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174016,GSM5174016: miRNA BDE 47 rep4; Danio rerio; miRNA Seq,GSM5174016,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174016,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s020-indexRPI20-GTGGCC-44_S20_L001_R1_001.fastq.gz,fastq,990919989.0,9811089.0,GSM5174016 r1,0:101 1:0,A:281268229;C:247800394;G:221010761;T:240816791;N:23814,101,0,,,281268229,247800394,221010761,240816791,23814,SRX10356637,SRS8474593,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00016,,0.0,,0.99965,,0.7,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63680,SRR13979075,SRX10356636,SRS8474592,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep3,GSM5174015,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174015,GSM5174015: miRNA BDE 47 rep3; Danio rerio; miRNA Seq,GSM5174015,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174015,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s019-indexRPI19-GTGAAA-43_S19_L001_R1_001.fastq.gz,fastq,936520278.0,9272478.0,GSM5174015 r1,0:101 1:0,A:292610982;C:215924738;G:200657250;T:227310895;N:16413,101,0,,,292610982,215924738,200657250,227310895,16413,SRX10356636,SRS8474592,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00017,,0.0,,0.99961,,0.6,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63681,SRR13979074,SRX10356635,SRS8474591,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep2,GSM5174014,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174014,GSM5174014: miRNA BDE 47 rep2; Danio rerio; miRNA Seq,GSM5174014,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174014,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s018-indexRPI18-GTCCGC-42_S18_L001_R1_001.fastq.gz,fastq,923871038.0,9147238.0,GSM5174014 r1,0:101 1:0,A:261826604;C:240583077;G:197471686;T:223966265;N:23406,101,0,,,261826604,240583077,197471686,223966265,23406,SRX10356635,SRS8474591,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,0.0,,0.99963,,0.70588,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63682,SRR13979073,SRX10356634,SRS8474588,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep1,GSM5174013,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174013,GSM5174013: miRNA BDE 47 rep1; Danio rerio; miRNA Seq,GSM5174013,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174013,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s017-indexRPI17-GTAGAG-41_S17_L001_R1_001.fastq.gz,fastq,963214780.0,9536780.0,GSM5174013 r1,0:101 1:0,A:290268878;C:222146596;G:216903245;T:233878186;N:17875,101,0,,,290268878,222146596,216903245,233878186,17875,SRX10356634,SRS8474588,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99971,,0.58333,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63683,SRR13979072,SRX10356633,SRS8474589,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep4,GSM5174012,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174012,GSM5174012: miRNA Control rep4; Danio rerio; miRNA Seq,GSM5174012,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174012,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s004-indexRPI4-TGACCA-4_S4_L001_R1_001.fastq.gz,fastq,776677274.0,7689874.0,GSM5174012 r1,0:101 1:0,A:233505881;C:196049592;G:158864473;T:188241779;N:15549,101,0,,,233505881,196049592,158864473,188241779,15549,SRX10356633,SRS8474589,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,0.0,,0.99949,,0.76086,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63684,SRR13979071,SRX10356632,SRS8474590,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep3,GSM5174011,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174011,GSM5174011: miRNA Control rep3; Danio rerio; miRNA Seq,GSM5174011,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174011,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s003-indexRPI3-TTAGGC-3_S3_L001_R1_001.fastq.gz,fastq,489457615.0,4846115.0,GSM5174011 r1,0:101 1:0,A:141598763;C:118796680;G:105152559;T:123899061;N:10552,101,0,,,141598763,118796680,105152559,123899061,10552,SRX10356632,SRS8474590,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00037,,0.0,,0.99947,,0.66666,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63685,SRR13979070,SRX10356631,SRS8474586,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep2,GSM5174010,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174010,GSM5174010: miRNA Control rep2; Danio rerio; miRNA Seq,GSM5174010,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174010,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s002-indexRPI2-CGATGT-2_S2_L001_R1_001.fastq.gz,fastq,777242066.0,7695466.0,GSM5174010 r1,0:101 1:0,A:226389551;C:187485077;G:166405949;T:196945091;N:16398,101,0,,,226389551,187485077,166405949,196945091,16398,SRX10356631,SRS8474586,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00026,,0.0,,0.99957,,0.62,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63686,SRR13979069,SRX10356630,SRS8474585,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep1,GSM5174009,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174009,GSM5174009: miRNA Control rep1; Danio rerio; miRNA Seq,GSM5174009,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174009,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s001-indexRPI1-ATCACG-1_S1_L001_R1_001.fastq.gz,fastq,370858163.0,3671863.0,GSM5174009 r1,0:101 1:0,A:112058381;C:93306905;G:75506546;T:89979021;N:7310,101,0,,,112058381,93306905,75506546,89979021,7310,SRX10356630,SRS8474585,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00033,,1e-05,,0.99949,,0.64516,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63794,SRR14066768,SRX10441285,SRS8573413,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 10,,strain:AB|isolate:WT24 small2|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr10,Bdnf Libr10,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,WT24_small2_R1_001.fastq.gz,fastq,1328140584.0,17475534.0,WT24 small2 R1 001.fastq.gz,0:76 1:0,A:412652031;C:328228938;G:257910677;T:329318258;N:30680,76,0,,,412652031,328228938,257910677,329318258,30680,SRX10441285,SRS8573413,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00121,,0.00038,,0.99918,,0.74603,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Multi-stage,Embryo,Whole Organism,All anatomical structures
63795,SRR14066769,SRX10441284,SRS8573412,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 9,,strain:AB|isolate:WT24 small1|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr9,Bdnf Libr9,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,WT24_small1_R1_001.fastq.gz,fastq,1219490832.0,16045932.0,WT24 small1 R1 001.fastq.gz,0:76 1:0,A:351083382;C:291591654;G:283111351;T:293679894;N:24551,76,0,,,351083382,291591654,283111351,293679894,24551,SRX10441284,SRS8573412,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00842,,0.00219,,0.99786,,0.61991,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Multi-stage,Embryo,Whole Organism,All anatomical structures
63802,SRR14066779,SRX10441277,SRS8573405,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 16,,strain:AB|isolate:MUT48 small4|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr16,Bdnf Libr16,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,MUT48_small4_R1_001.fastq.gz,fastq,1346335212.0,17714937.0,MUT48 small4 R1 001.fastq.gz,0:76 1:0,A:416374120;C:317460666;G:293419951;T:319049435;N:31040,76,0,,,416374120,317460666,293419951,319049435,31040,SRX10441277,SRS8573405,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00179,,0.00093,,0.99935,,0.5625,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Hatching,Embryo,Whole Organism,All anatomical structures
63803,SRR14066776,SRX10441276,SRS8573404,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 15,,strain:AB|isolate:MUT48 small3|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr15,Bdnf Libr15,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,MUT48_small3_R1_001.fastq.gz,fastq,1304806760.0,17168510.0,MUT48 small3 R1 001.fastq.gz,0:76 1:0,A:387991384;C:335175146;G:279195316;T:302418185;N:26729,76,0,,,387991384,335175146,279195316,302418185,26729,SRX10441276,SRS8573404,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00621,,0.00334,,0.99926,,0.64343,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Hatching,Embryo,Whole Organism,All anatomical structures
63804,SRR14066777,SRX10441275,SRS8573403,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 14,,strain:AB|isolate:WT48 small4|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr14,Bdnf Libr14,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,WT48_small4_R1_001.fastq.gz,fastq,1339796780.0,17628905.0,WT48 small4 R1 001.fastq.gz,0:76 1:0,A:416769744;C:315222509;G:273799428;T:333973227;N:31872,76,0,,,416769744,315222509,273799428,333973227,31872,SRX10441275,SRS8573403,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00503,,0.00127,,0.99888,,0.67632,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Hatching,Embryo,Whole Organism,All anatomical structures
63805,SRR14066778,SRX10441274,SRS8573402,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 13,,strain:AB|isolate:WT48 small3|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr13,Bdnf Libr13,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,WT48_small3_R1_001.fastq.gz,fastq,1212286260.0,15951135.0,WT48 small3 R1 001.fastq.gz,0:76 1:0,A:374600889;C:299473187;G:252454435;T:285727773;N:29976,76,0,,,374600889,299473187,252454435,285727773,29976,SRX10441274,SRS8573402,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.01297,,0.00494,,0.99849,,0.661,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Hatching,Embryo,Whole Organism,All anatomical structures
63806,SRR14066780,SRX10441273,SRS8573401,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 12,,strain:AB|isolate:MUT24 small2|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr12,Bdnf Libr12,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,MUT24_small2_R1_001.fastq.gz,fastq,1214643400.0,15982150.0,MUT24 small2 R1 001.fastq.gz,0:76 1:0,A:339563536;C:303989834;G:244843758;T:326220311;N:25961,76,0,,,339563536,303989834,244843758,326220311,25961,SRX10441273,SRS8573401,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00526,,0.00203,,0.99876,,0.62659,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Multi-stage,Embryo,Whole Organism,All anatomical structures
63807,SRR14066781,SRX10441272,SRS8573400,SRP312051,PRJNA716861,Zebrafish Bdnf CRISPR/CAS9 knock out,PRJNA716861,Other,RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish,,,,,SD 11,,strain:AB|isolate:MUT24 small1|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Danio rerio Bdnf mutant,Bdnf Libr11,Bdnf Libr11,Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP312051,,,MUT24_small1_R1_001.fastq.gz,fastq,1273652916.0,16758591.0,MUT24 small1 R1 001.fastq.gz,0:76 1:0,A:398579242;C:309782360;G:268224898;T:297035166;N:31250,76,0,,,398579242,309782360,268224898,297035166,31250,SRX10441272,SRS8573400,SRA1209895,Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms,Stazione Zoologica Anton Dohrn,1,0.00191,,0.0006,,0.9992,,0.60752,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Italy,2021-03-25,Multi-stage,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