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156 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "miRNA-Seq" and tissue_curation = "Whole Organism"

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experiment.library_selection 5

devstage_curation 5

experiment.platform 3

devstage_curation_coarse 3

technology 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 156 ✖

experiment.library_strategy 1

  • miRNA-Seq · 156 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 156 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 41247 SRR3953258 SRX1977494 SRS1585137 SRP079896 PRJNA335352 Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment GSE84845 Transcriptome Analysis Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.   pubmed:28072866   c Wildtype miRNA GSM2252181   source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf c Wildtype miRNA Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample. 6 dpf larvae   Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.   strain:Tuebingen|tissue:whole larvae|age:6 dpf GSM2252181 GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq GSM2252181   1 Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2252181 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP079896     Sample_c_1_filtered.fastq.gz fastq 413922462.0 17365113.0 GSM2252181 r1 0:23.84 1:0 A:102173642;C:93233248;G:103684592;T:114815345;N:15635 23 0     102173642 93233248 103684592 114815345 15635 SRX1977494 SRS1585137 SRA444471 GEO Tongji University 1 0.85083   0.06831   0.88152   0.63274   27   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-26 Larval Larval Whole Organism All anatomical structures
41457 41457 SRR4449278 SRX2267734 SRS1758938 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S09 RID0445   strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S09 S09 RID0445 S09 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_009_rawlib.basecaller.bam bam 56886794.0 2186951.0 IonXpressRNA 009 rawlib.basecaller.bam 0:26.01 A:15763527;C:12934017;G:13233004;T:14956246;N:0 26       15763527 12934017 13233004 14956246 0 SRX2267734 SRS1758938 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.6501   0.44849   0.83465   0.59625   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2016-10-25 Gastrula Embryo Whole Organism All anatomical structures
41458 41458 SRR4449277 SRX2267733 SRS1758937 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S10 RID0445   strain:ABTL|dev stage:51% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S10 S10 RID0445 S10 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_010_rawlib.basecaller.bam bam 63108712.0 2361941.0 IonXpressRNA 010 rawlib.basecaller.bam 0:26.72 A:16956361;C:14496251;G:15049416;T:16606684;N:0 26       16956361 14496251 15049416 16606684 0 SRX2267733 SRS1758937 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.64387   0.42592   0.81091   0.58276   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41459 41459 SRR4449276 SRX2267732 SRS1758936 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S07 RID0445   strain:ABTL|dev stage:47% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S07 S07 RID0445 S07 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_007_rawlib.basecaller.bam bam 50356775.0 1885340.0 IonXpressRNA 007 rawlib.basecaller.bam 0:26.71 A:13603929;C:11508700;G:12096780;T:13147366;N:0 26       13603929 11508700 12096780 13147366 0 SRX2267732 SRS1758936 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.63582   0.39586   0.79839   0.56846   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41460 41460 SRR4449275 SRX2267731 SRS1758935 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S08 RID0445   strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S08 S08 RID0445 S08 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_008_rawlib.basecaller.bam bam 63655011.0 2486240.0 IonXpressRNA 008 rawlib.basecaller.bam 0:25.60 A:17274215;C:14286496;G:15277222;T:16817078;N:0 25       17274215 14286496 15277222 16817078 0 SRX2267731 SRS1758935 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.64165   0.41617   0.79931   0.56754   34   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41461 41461 SRR4449274 SRX2267730 SRS1758933 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S05 RID0445   strain:ABTL|dev stage:58% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S05 S05 RID0445 S05 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_005_rawlib.basecaller.bam bam 36352941.0 1403002.0 IonXpressRNA 005 rawlib.basecaller.bam 0:25.91 A:10088289;C:8176923;G:8667822;T:9419907;N:0 25       10088289 8176923 8667822 9419907 0 SRX2267730 SRS1758933 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.59289   0.36407   0.80213   0.57695   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41462 41462 SRR4449273 SRX2267729 SRS1758934 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S06 RID0445   strain:ABTL|dev stage:43% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S06 S06 RID0445 S06 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_006_rawlib.basecaller.bam bam 41157611.0 1592351.0 IonXpressRNA 006 rawlib.basecaller.bam 0:25.85 A:11322629;C:9228187;G:9750979;T:10855816;N:0 25       11322629 9228187 9750979 10855816 0 SRX2267729 SRS1758934 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.63095   0.40683   0.8003   0.56985   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41463 41463 SRR4449272 SRX2267728 SRS1758932 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S03 RID0445   strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S03 S03 RID0445 S03 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_003_rawlib.basecaller.bam bam 60356442.0 2057592.0 IonXpressRNA 003 rawlib.basecaller.bam 0:29.33 A:17060096;C:13661341;G:13721228;T:15913777;N:0 29       17060096 13661341 13721228 15913777 0 SRX2267728 SRS1758932 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.73029   0.49935   0.8225   0.56029   30   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41464 41464 SRR4449271 SRX2267727 SRS1758931 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S04 RID0445   strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S04 S04 RID0445 S04 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_004_rawlib.basecaller.bam bam 55705225.0 2055064.0 IonXpressRNA 004 rawlib.basecaller.bam 0:27.11 A:15806355;C:12308008;G:12579212;T:15011650;N:0 27       15806355 12308008 12579212 15011650 0 SRX2267727 SRS1758931 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.70796   0.49815   0.81444   0.54452   41   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41465 41465 SRR4449270 SRX2267726 SRS1758930 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S01 RID0445   strain:ABTL|dev stage:50% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S01 S01 RID0445 S01 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_001_rawlib.basecaller.bam bam 35407241.0 1342552.0 IonXpressRNA 001 rawlib.basecaller.bam 0:26.37 A:9988109;C:7841340;G:8187069;T:9390723;N:0 26       9988109 7841340 8187069 9390723 0 SRX2267726 SRS1758930 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.63621   0.43661   0.80992   0.53899   31   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41466 41466 SRR4449269 SRX2267725 SRS1758928 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S02 RID0445   strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S02 S02 RID0445 S02 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_002_rawlib.basecaller.bam bam 40875445.0 1512601.0 IonXpressRNA 002 rawlib.basecaller.bam 0:27.02 A:11593378;C:9124451;G:9444184;T:10713432;N:0 27       11593378 9124451 9444184 10713432 0 SRX2267725 SRS1758928 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.66621   0.45417   0.8127   0.55033   21   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41467 41467 SRR4449267 SRX2267724 SRS1758927 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S15 RID0445   strain:ABTL|dev stage:52% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S15 S15 RID0445 S15 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_015_rawlib.basecaller.bam bam 58421266.0 2091074.0 IonXpressRNA 015 rawlib.basecaller.bam 0:27.94 A:16715618;C:13019609;G:13014639;T:15671400;N:0 27       16715618 13019609 13014639 15671400 0 SRX2267724 SRS1758927 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.71786   0.51457   0.83863   0.53442   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41468 41468 SRR4449266 SRX2267723 SRS1758929 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S16 RID0445   strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S16 S16 RID0445 S16 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_016_rawlib.basecaller.bam bam 55022551.0 2073507.0 IonXpressRNA 016 rawlib.basecaller.bam 0:26.54 A:15319738;C:12288588;G:12653066;T:14761159;N:0 26       15319738 12288588 12653066 14761159 0 SRX2267723 SRS1758929 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.68905   0.46941   0.80306   0.55981   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41469 41469 SRR4449265 SRX2267722 SRS1758926 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S13 RID0445   strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S13 S13 RID0445 S13 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_013_rawlib.basecaller.bam bam 49641484.0 2028008.0 IonXpressRNA 013 rawlib.basecaller.bam 0:24.48 A:13840820;C:11016762;G:11715475;T:13068427;N:0 24       13840820 11016762 11715475 13068427 0 SRX2267722 SRS1758926 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.55355   0.3659   0.81576   0.55987   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41470 41470 SRR4449264 SRX2267721 SRS1758925 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S14 RID0445   strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S14 S14 RID0445 S14 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_014_rawlib.basecaller.bam bam 52969826.0 2019609.0 IonXpressRNA 014 rawlib.basecaller.bam 0:26.23 A:14762618;C:11847782;G:12164393;T:14195033;N:0 26       14762618 11847782 12164393 14195033 0 SRX2267721 SRS1758925 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.65926   0.45113   0.80515   0.56221   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41471 41471 SRR4449263 SRX2267720 SRS1758923 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S11 RID0445   strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S11 S11 RID0445 S11 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_011_rawlib.basecaller.bam bam 54877334.0 2122171.0 IonXpressRNA 011 rawlib.basecaller.bam 0:25.86 A:14884144;C:12539815;G:13173981;T:14279394;N:0 25       14884144 12539815 13173981 14279394 0 SRX2267720 SRS1758923 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.62581   0.40704   0.82002   0.59605   20   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
41472 41472 SRR4449262 SRX2267719 SRS1758924 SRP092030 PRJNA350377 Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly PRJNA350377 Transcriptome Analysis Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly     Danio rerio embryo at approx. 50% epiboly Danio rerio embryo at approx. 50% epiboly S12 RID0445   strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 S12 S12 RID0445 S12 RID0445 Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP092030     IonXpressRNA_012_rawlib.basecaller.bam bam 51987914.0 1937451.0 IonXpressRNA 012 rawlib.basecaller.bam 0:26.83 A:14499922;C:11778716;G:11957347;T:13751929;N:0 26       14499922 11778716 11957347 13751929 0 SRX2267719 SRS1758924 SRA486759 UNIVERSITY OF AMSTERDAM, SILS|RB&amp;AB UNIVERSITY OF AMSTERDAM, SILS 1 0.67286   0.44698   0.80919   0.58291   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2017-11-01 Gastrula Embryo Whole Organism All anatomical structures
53033 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   pubmed:33602989   F1 Control1 nmbu sncRNA 1 GSM4605877   tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents F1 Control1 nmbu sncRNA 1 Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values Whole embryo   Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.   develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents GSM4605877 GSM4605877: F1 Control1 nmbu sncRNA 1; Danio rerio; miRNA Seq GSM4605877   1 Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material. GEO Accession:GSM4605877 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 4000   SRP266770     nmbu_sncRNA_1_raw.fq.gz fastq 534855250.0 10697105.0 GSM4605877 r1 0:50 A:156249541;C:120087413;G:145230236;T:113171967;N:116093 50       156249541 120087413 145230236 113171967 116093 SRX8518000 SRS6815481 SRA1085407 GEO Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences 1 0.74031   0.40182   0.83366   0.60438   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Norway 2020-06-10 Gastrula Embryo Whole Organism All anatomical structures
60445 60445 SRR12272862 SRX8777892 SRS7048444 SRP272672 PRJNA647444 mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA PRJNA647444 Other Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.       C2 C2 C2 2 4   replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C2C220200712 C2C220200712 RNA seq of zebrafish in different conditions     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP272672   loader:fastq load.py C2_C2_2_4.fq fastq 542610936.0 21965958.0 C2 C2 2 4.fq.gz 0:24.70 A:95221617;C:122628624;G:167025611;T:157730855;N:4229 24       95221617 122628624 167025611 157730855 4229 SRX8777892 SRS7048444 SRA1101037 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.8119   0.10745   0.85717   0.51338   22   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-08-05 Undetermined Embryo Whole Organism All anatomical structures
60446 60446 SRR12272863 SRX8777891 SRS7048443 SRP272672 PRJNA647444 mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA PRJNA647444 Other Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.       C2 C2 C2 1 4   replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C2C220200711 C2C220200711 RNA seq of zebrafish in different conditions     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP272672   loader:fastq load.py C2_C2_1_4.fq fastq 542847476.0 22614181.0 C2 C2 1 4.fq.gz 0:24.00 A:99999101;C:125407906;G:162383758;T:155055099;N:1612 24       99999101 125407906 162383758 155055099 1612 SRX8777891 SRS7048443 SRA1101037 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.84327   0.10491   0.83256   0.52046   19   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-08-05 Undetermined Embryo Whole Organism All anatomical structures
60447 60447 SRR12272864 SRX8777890 SRS7048442 SRP272672 PRJNA647444 mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA PRJNA647444 Other Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.       C1 C1 C1 2 4   replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C1C120200712 C1C120200712 RNA seq of zebrafish in different conditions     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP272672   loader:fastq load.py C1_C1_2_4.fq fastq 570918284.0 22577002.0 C1 C1 2 4.fq.gz 0:25.29 A:100121235;C:130480588;G:178656113;T:161652765;N:7583 25       100121235 130480588 178656113 161652765 7583 SRX8777890 SRS7048442 SRA1101037 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.85096   0.12542   0.82873   0.51535   22   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-08-05 Undetermined Embryo Whole Organism All anatomical structures
60448 60448 SRR12272865 SRX8777889 SRS7048441 SRP272672 PRJNA647444 mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA PRJNA647444 Other Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.       C1 C1 C1 1 4   replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C1C120200711 C1C120200711 RNA seq of zebrafish in different conditions     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP272672   loader:fastq load.py C1_C1_1_4.fq fastq 545089417.0 22812164.0 C1 C1 1 4.fq.gz 0:23.89 A:99851844;C:125314095;G:166401335;T:153521167;N:976 23       99851844 125314095 166401335 153521167 976 SRX8777889 SRS7048441 SRA1101037 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.84602   0.11725   0.83159   0.51353   19   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-08-05 Undetermined Embryo Whole Organism All anatomical structures
60449 60449 SRR12272866 SRX8777888 SRS7048440 SRP272672 PRJNA647444 mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA PRJNA647444 Other Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.       C0 C0 C0 2 4   replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C0C020200712 C0C020200712 RNA seq of zebrafish in different conditions     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP272672   loader:fastq load.py C0_C0_2_4.fq fastq 527443144.0 23174740.0 C0 C0 2 4.fq.gz 0:22.76 A:102368401;C:120843229;G:151690193;T:152540806;N:515 22       102368401 120843229 151690193 152540806 515 SRX8777888 SRS7048440 SRA1101037 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.83063   0.08114   0.85169   0.50894   16   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-08-05 Undetermined Embryo Whole Organism All anatomical structures
60450 60450 SRR12272867 SRX8777887 SRS7048439 SRP272672 PRJNA647444 mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA PRJNA647444 Other Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.       C0 C0 C0 1 4   replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C0C020200711 C0C020200711 RNA seq of zebrafish in different conditions     miRNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP272672   loader:fastq load.py C0_C0_1_4.fq fastq 511759408.0 22673361.0 C0 C0 1 4.fq.gz 0:22.57 A:100879182;C:120237907;G:142799495;T:147842595;N:229 22       100879182 120237907 142799495 147842595 229 SRX8777887 SRS7048439 SRA1101037 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.83904   0.0823   0.84741   0.49929   22   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-08-05 Undetermined Embryo Whole Organism All anatomical structures
63643 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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 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 con…   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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;