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
6,DRR315802,DRX305194,DRS231989,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample4,SAMD00400823,,sample name:rw147 2.5dpf wildtype  rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,DRX305194,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,,,,10262353995.0,34151547.0,DRR315802,0:150.27 1:150.22,A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550,150,150,,,2735078560,2386126821,2433638250,2707202814,307550,DRX305194,DRS231989,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95231,0.95295,0.09229,0.08773,0.71819,0.72107,0.46746,0.46617,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
7,DRR315801,DRX305193,DRS231988,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample3,SAMD00400822,,sample name:rw147 2.5dpf wildtype  rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,DRX305193,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,,,,11516368634.0,38355888.0,DRR315801,0:150.15 1:150.10,A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954,150,150,,,3080341643,2678048339,2713051368,3044449330,477954,DRX305193,DRS231988,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95353,0.95634,0.08909,0.08533,0.71374,0.71252,0.45986,0.46059,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
8,DRR315800,DRX305192,DRS231987,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample2,SAMD00400821,,sample name:rw147 2.5dpf wildtype  rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,DRX305192,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,,,,8814057148.0,29367513.0,DRR315800,0:150.09 1:150.04,A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957,150,150,,,2350403211,2054073465,2083044327,2326181188,354957,DRX305192,DRS231987,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95287,0.95643,0.0891,0.08586,0.70309,0.70252,0.46384,0.46281,151,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
9,DRR315799,DRX305191,DRS231986,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample1,SAMD00400820,,sample name:rw147 2.5dpf wildtype  rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,DRX305191,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,,,,10491955578.0,34900682.0,DRR315799,0:150.34 1:150.28,A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831,150,150,,,2796521111,2446218287,2483414564,2765477785,323831,DRX305191,DRS231986,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9539,0.95646,0.08185,0.07808,0.70025,0.70013,0.44713,0.44987,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
10,DRR315798,DRX305190,DRS231985,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample4,SAMD00400819,,sample name:rw147 2.5dpf Mutant  rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,DRX305190,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,,,,9197802250.0,30604326.0,DRR315798,0:150.30 1:150.24,A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028,150,150,,,2468967963,2130949980,2158692262,2438931017,261028,DRX305190,DRS231985,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95159,0.95439,0.10146,0.09758,0.71995,0.71983,0.46519,0.46797,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
11,DRR315797,DRX305189,DRS231984,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample3,SAMD00400818,,sample name:rw147 2.5dpf Mutant  rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,DRX305189,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,,,,10498982078.0,34931731.0,DRR315797,0:150.31 1:150.25,A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945,150,150,,,2804535103,2445295179,2478768789,2770066062,316945,DRX305189,DRS231984,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95448,0.95652,0.0939,0.0887,0.71796,0.71847,0.46335,0.46615,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
12,DRR315796,DRX305188,DRS231983,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample2,SAMD00400817,,sample name:rw147 2.5dpf Mutant  rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,DRX305188,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,,,,9850145990.0,32782079.0,DRR315796,0:150.26 1:150.21,A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024,150,150,,,2636205537,2286508705,2319481100,2607600624,350024,DRX305188,DRS231983,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95193,0.95472,0.09722,0.09375,0.7138,0.71299,0.45542,0.45994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
13,DRR315795,DRX305187,DRS231982,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample1,SAMD00400816,,sample name:rw147 2.5dpf Mutant  rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,DRX305187,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,,,,9542039835.0,31780260.0,DRR315795,0:150.15 1:150.10,A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225,150,150,,,2543384204,2224374632,2258183435,2515655339,442225,DRX305187,DRS231982,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9528,0.95591,0.08656,0.0828,0.70352,0.70331,0.45316,0.44914,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
30035,SRR27732031,SRX23397617,SRS20258458,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 48 hpf embryo,zebrafish embryo 48hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 18,W 18,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT48h-3_1.fq.gz WT48h-3_2.fq.gz,fastq fastq,6520477800.0,21734926.0,WT48h 3 1.fq.gz,0:150 1:150,A:1739928482;C:1516508736;G:1531638319;T:1732180903;N:221360,150,150,,,1739928482,1516508736,1531638319,1732180903,221360,SRX23397617,SRS20258458,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93874,0.93954,0.09485,0.09438,0.67888,0.67913,0.46039,0.46026,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30036,SRR27732032,SRX23397616,SRS20258457,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 48 hpf embryo,zebrafish embryo 48hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 17,W 17,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT48h-2_2.fq.gz WT48h-2_1.fq.gz,fastq fastq,7046397300.0,23487991.0,WT48h 2 1.fq.gz,0:150 1:150,A:1865031055;C:1655796645;G:1670091105;T:1855237793;N:240702,150,150,,,1865031055,1655796645,1670091105,1855237793,240702,SRX23397616,SRS20258457,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94056,0.93987,0.08562,0.08535,0.68241,0.68288,0.46355,0.46204,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30037,SRR27732033,SRX23397615,SRS20258456,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 48 hpf embryo,zebrafish embryo 48hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 16,W 16,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT48h-1_1.fq.gz WT48h-1_2.fq.gz,fastq fastq,6851959800.0,22839866.0,WT48h 1 1.fq.gz,0:150 1:150,A:1813160204;C:1610483050;G:1626359291;T:1801871129;N:86126,150,150,,,1813160204,1610483050,1626359291,1801871129,86126,SRX23397615,SRS20258456,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94028,0.93857,0.08526,0.08523,0.68331,0.68477,0.45695,0.45202,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30053,SRR27730716,SRX23396342,SRS20257256,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  48 hpf embryo,zebrafish embryo hamp /  48hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 39,W 39,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp48h-3_1.fq.gz hamp48h-3_2.fq.gz,fastq fastq,7580570700.0,25268569.0,hamp48h 3 1.fq.gz,0:150 1:150,A:2019162299;C:1768225001;G:1782049665;T:2011039613;N:94122,150,150,,,2019162299,1768225001,1782049665,2011039613,94122,SRX23396342,SRS20257256,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93863,0.93681,0.08675,0.08582,0.68394,0.6857,0.46373,0.46321,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30054,SRR27730717,SRX23396341,SRS20257255,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  48 hpf embryo,zebrafish embryo hamp /  48hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 38,W 38,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp48h-2_1.fq.gz hamp48h-2_2.fq.gz,fastq fastq,7385330400.0,24617768.0,hamp48h 2 1.fq.gz,0:150 1:150,A:1971527478;C:1717463447;G:1738237873;T:1957858394;N:243208,150,150,,,1971527478,1717463447,1738237873,1957858394,243208,SRX23396341,SRS20257255,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93851,0.9369,0.09049,0.08988,0.68274,0.6843,0.45945,0.46042,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30055,SRR27730718,SRX23396340,SRS20257254,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  48 hpf embryo,zebrafish embryo hamp /  48hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 37,W 37,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp48h-1_1.fq.gz hamp48h-1_2.fq.gz,fastq fastq,6188343000.0,20627810.0,hamp48h 1 1.fq.gz,0:150 1:150,A:1649030143;C:1444577102;G:1461592285;T:1633092294;N:51176,150,150,,,1649030143,1444577102,1461592285,1633092294,51176,SRX23396340,SRS20257254,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94313,0.94006,0.08835,0.08702,0.6859,0.68702,0.45658,0.46001,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35460,SRR32818804,SRX28102240,SRS24458287,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 8,GSM8863198,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 8,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863198,GSM8863198: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 8; Danio rerio; RNA Seq,GSM8863198 r1,GSM8863198,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P57-GTTCCAAT-GCAGAATT-READ1-Sequences.txt nR284-L2-G5-P57-GTTCCAAT-GCAGAATT-READ2-Sequences.txt,fastq fastq,10743485140.0,53185570.0,GSM8863198 r1,0:101 1:101,A:2043166141;C:3372557345;G:3302778932;T:2024928209;N:54513,101,101,,,2043166141,3372557345,3302778932,2024928209,54513,SRX28102240,SRS24458287,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35461,SRR32818805,SRX28102239,SRS24458286,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 7,GSM8863197,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 7,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863197,GSM8863197: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 7; Danio rerio; RNA Seq,GSM8863197 r1,GSM8863197,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P56-GCAATGCA-AACGTTCC-READ1-Sequences.txt nR284-L2-G5-P56-GCAATGCA-AACGTTCC-READ2-Sequences.txt,fastq fastq,8690926174.0,43024387.0,GSM8863197 r1,0:101 1:101,A:1676436454;C:2706306943;G:2647919752;T:1660219021;N:44004,101,101,,,1676436454,2706306943,2647919752,1660219021,44004,SRX28102239,SRS24458286,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35462,SRR32818806,SRX28102238,SRS24458285,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 6,GSM8863196,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 6,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863196,GSM8863196: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 6; Danio rerio; RNA Seq,GSM8863196 r1,GSM8863196,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P55-ATGGCATG-GGTACCTT-READ1-Sequences.txt nR284-L2-G5-P55-ATGGCATG-GGTACCTT-READ2-Sequences.txt,fastq fastq,10679789894.0,52870247.0,GSM8863196 r1,0:101 1:101,A:2075736321;C:3306230069;G:3245751043;T:2052019154;N:53307,101,101,,,2075736321,3306230069,3245751043,2052019154,53307,SRX28102238,SRS24458285,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35463,SRR32818807,SRX28102237,SRS24458284,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5,GSM8863195,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863195,GSM8863195: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5; Danio rerio; RNA Seq,GSM8863195 r1,GSM8863195,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P54-GGAGCGTC-GCACGGAC-READ1-Sequences.txt nR284-L2-G5-P54-GGAGCGTC-GCACGGAC-READ2-Sequences.txt,fastq fastq,10631975484.0,52633542.0,GSM8863195 r1,0:101 1:101,A:1978520961;C:3379107355;G:3313372052;T:1960921814;N:53302,101,101,,,1978520961,3379107355,3313372052,1960921814,53302,SRX28102237,SRS24458284,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35464,SRR32818808,SRX28102236,SRS24458283,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4,GSM8863194,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863194,GSM8863194: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4; Danio rerio; RNA Seq,GSM8863194 r1,GSM8863194,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P53-AAGATACT-ATGTAAGT-READ1-Sequences.txt nR284-L2-G5-P53-AAGATACT-ATGTAAGT-READ2-Sequences.txt,fastq fastq,11273189336.0,55807868.0,GSM8863194 r1,0:101 1:101,A:2204760360;C:3477277778;G:3404605220;T:2186489012;N:56966,101,101,,,2204760360,3477277778,3404605220,2186489012,56966,SRX28102236,SRS24458283,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35465,SRR32818809,SRX28102235,SRS24458282,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 3,GSM8863193,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 3,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863193,GSM8863193: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 3; Danio rerio; RNA Seq,GSM8863193 r1,GSM8863193,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P52-GCGCAAGC-CGGCGTGA-READ1-Sequences.txt nR284-L2-G5-P52-GCGCAAGC-CGGCGTGA-READ2-Sequences.txt,fastq fastq,10239163658.0,50688929.0,GSM8863193 r1,0:101 1:101,A:2004831470;C:3154126629;G:3091862970;T:1988292042;N:50547,101,101,,,2004831470,3154126629,3091862970,1988292042,50547,SRX28102235,SRS24458282,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35466,SRR32818810,SRX28102234,SRS24458281,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 2,GSM8863192,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 2,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863192,GSM8863192: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 2; Danio rerio; RNA Seq,GSM8863192 r1,GSM8863192,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P51-ATATGGAT-TAATACAG-READ1-Sequences.txt nR284-L2-G5-P51-ATATGGAT-TAATACAG-READ2-Sequences.txt,fastq fastq,11426211002.0,56565401.0,GSM8863192 r1,0:101 1:101,A:2181426814;C:3575345894;G:3505040965;T:2164340511;N:56818,101,101,,,2181426814,3575345894,3505040965,2164340511,56818,SRX28102234,SRS24458281,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35467,SRR32818811,SRX28102233,SRS24458280,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 1,GSM8863191,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 1,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control,GSM8863191,GSM8863191: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 1; Danio rerio; RNA Seq,GSM8863191 r1,GSM8863191,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P50-CGGACAAC-AATCCGGA-READ1-Sequences.txt nR284-L2-G5-P50-CGGACAAC-AATCCGGA-READ2-Sequences.txt,fastq fastq,8241627270.0,40800135.0,GSM8863191 r1,0:101 1:101,A:1585704825;C:2569399779;G:2515169694;T:1571311579;N:41393,101,101,,,1585704825,2569399779,2515169694,1571311579,41393,SRX28102233,SRS24458280,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35468,SRR32818812,SRX28102232,SRS24458279,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 6,GSM8863190,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 6,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage,GSM8863190,GSM8863190: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 6; Danio rerio; RNA Seq,GSM8863190 r1,GSM8863190,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P49-TAAGTGGT-GGCTTAAG-READ1-Sequences.txt nR284-L2-G5-P49-TAAGTGGT-GGCTTAAG-READ2-Sequences.txt,fastq fastq,11020907900.0,54558950.0,GSM8863190 r1,0:101 1:101,A:2122315499;C:3428329681;G:3363708951;T:2106499941;N:53828,101,101,,,2122315499,3428329681,3363708951,2106499941,53828,SRX28102232,SRS24458279,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35469,SRR32818813,SRX28102231,SRS24458278,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5,GSM8863189,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage,GSM8863189,GSM8863189: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5; Danio rerio; RNA Seq,GSM8863189 r1,GSM8863189,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P48-TACCGAGG-AGTTCAGG-READ1-Sequences.txt nR284-L2-G5-P48-TACCGAGG-AGTTCAGG-READ2-Sequences.txt,fastq fastq,9778516798.0,48408499.0,GSM8863189 r1,0:101 1:101,A:1871707305;C:3053861632;G:3000334130;T:1852564463;N:49268,101,101,,,1871707305,3053861632,3000334130,1852564463,49268,SRX28102231,SRS24458278,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35470,SRR32818814,SRX28102230,SRS24458277,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4,GSM8863188,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage,GSM8863188,GSM8863188: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4; Danio rerio; RNA Seq,GSM8863188 r1,GSM8863188,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P47-AATGCCTC-TGGATCGA-READ1-Sequences.txt nR284-L2-G5-P47-AATGCCTC-TGGATCGA-READ2-Sequences.txt,fastq fastq,9225871462.0,45672631.0,GSM8863188 r1,0:101 1:101,A:1812334628;C:2836256230;G:2784608990;T:1792625480;N:46134,101,101,,,1812334628,2836256230,2784608990,1792625480,46134,SRX28102230,SRS24458277,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35471,SRR32818815,SRX28102229,SRS24458276,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 3,GSM8863187,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 3,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage,GSM8863187,GSM8863187: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 3; Danio rerio; RNA Seq,GSM8863187 r1,GSM8863187,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P46-GGCATTCT-CAAGCTAG-READ1-Sequences.txt nR284-L2-G5-P46-GGCATTCT-CAAGCTAG-READ2-Sequences.txt,fastq fastq,8722157192.0,43178996.0,GSM8863187 r1,0:101 1:101,A:1656516190;C:2739809093;G:2694619623;T:1631169000;N:43286,101,101,,,1656516190,2739809093,2694619623,1631169000,43286,SRX28102229,SRS24458276,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35472,SRR32818816,SRX28102228,SRS24458275,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 2,GSM8863186,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 2,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage,GSM8863186,GSM8863186: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 2; Danio rerio; RNA Seq,GSM8863186 r1,GSM8863186,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P45-TTACAGGA-GCTTGTCA-READ1-Sequences.txt nR284-L2-G5-P45-TTACAGGA-GCTTGTCA-READ2-Sequences.txt,fastq fastq,9539410206.0,47224803.0,GSM8863186 r1,0:101 1:101,A:1827192429;C:2980924877;G:2922457892;T:1808788630;N:46378,101,101,,,1827192429,2980924877,2922457892,1808788630,46378,SRX28102228,SRS24458275,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
35473,SRR32818817,SRX28102227,SRS24458274,SRP572436,PRJNA1240804,Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset,GSE292683,Transcriptome Analysis,Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.,,pubmed:40145570,,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 1,GSM8863185,,source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing,sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 1,Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts,FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos,,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O’Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage,GSM8863185,GSM8863185: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 1; Danio rerio; RNA Seq,GSM8863185 r1,GSM8863185,1,For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP572436,,,nR284-L2-G5-P44-CCGTGAAG-ATCCACTG-READ1-Sequences.txt nR284-L2-G5-P44-CCGTGAAG-ATCCACTG-READ2-Sequences.txt,fastq fastq,8772356010.0,43427505.0,GSM8863185 r1,0:101 1:101,A:1656754122;C:2760877460;G:2711917989;T:1642763644;N:42795,101,101,,,1656754122,2760877460,2711917989,1642763644,42795,SRX28102227,SRS24458274,SRA2098459,UC Irvine,UC Irvine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,United States,2025-03-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36373,SRR499871,SRX148961,SRS334490,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 48h silver ions,GSM935123,,source name:Dre 48h silver ions|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver ions 0.25 µg/L of silver nitrate|barcode:GCGA,Dre 48h silver ions,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 48h silver ions,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver ions 0.25 µg/L of silver nitrate|barcode:GCGA,GSM935123,GSM935123: Dre 48h silver ions; Danio rerio; OTHER,GSM935123 1,GSM935123: Dre 48h silver ions,1,,GEO Accession:GSM935123,OTHER,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>,SRP013309,,,Dre_48h_ag.gz,fastq,85514364.0,2375399.0,GSM935123 r1,0:36,A:18075876;C:24481350;G:23393114;T:19494907;N:69117,36,,,,18075876,24481350,23393114,19494907,69117,SRX148961,SRS334490,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.11101,,0.00946,,0.96224,,0.6991,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Hatching,Embryo,Whole Organism,All anatomical structures
36374,SRR499870,SRX148960,SRS334489,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 48h silver bulk,GSM935122,,source name:Dre 48h silver bulk|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver bulk 0.6 1.6µm; 5 µg/L|barcode:GCGC,Dre 48h silver bulk,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 48h silver bulk,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver bulk 0.6 1.6µm; 5 µg/L|barcode:GCGC,GSM935122,GSM935122: Dre 48h silver bulk; Danio rerio; OTHER,GSM935122 1,GSM935122: Dre 48h silver bulk,1,,GEO Accession:GSM935122,OTHER,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>,SRP013309,,,Dre_48h_bulk.gz,fastq,95750712.0,2659742.0,GSM935122 r1,0:36,A:17624901;C:29735122;G:26376026;T:21938121;N:76542,36,,,,17624901,29735122,26376026,21938121,76542,SRX148960,SRS334489,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.18319,,0.01693,,0.94391,,0.57004,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Hatching,Embryo,Whole Organism,All anatomical structures
36375,SRR499869,SRX148959,SRS334488,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 48h silver NP,GSM935121,,source name:Dre 48h silver NP|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver nanoparticles 10nm; 5µg/L|barcode:GCTG,Dre 48h silver NP,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 48h silver NP,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver nanoparticles 10nm; 5µg/L|barcode:GCTG,GSM935121,GSM935121: Dre 48h silver NP; Danio rerio; OTHER,GSM935121 1,GSM935121: Dre 48h silver NP,1,,GEO Accession:GSM935121,OTHER,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>,SRP013309,,,Dre_48h_NP.gz,fastq,52931304.0,1470314.0,GSM935121 r1,0:36,A:10003539;C:15279729;G:14487570;T:13116768;N:43698,36,,,,10003539,15279729,14487570,13116768,43698,SRX148959,SRS334488,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.14206,,0.01226,,0.95477,,0.58652,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Hatching,Embryo,Whole Organism,All anatomical structures
36376,SRR499868,SRX148958,SRS334487,SRP013309,PRJNA167302,Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform,GSE38125,Other,Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.,,pubmed:23758687,,Dre 48h control,GSM935120,,source name:Dre 48h control|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:control|barcode:GCTT,Dre 48h control,FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library,Dre 48h control,Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 µg/L of 10nm Ag NP  5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80°C for analysis of gene expression. The experiment was terminated at 48 hpf.,High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.,Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.,strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:control|barcode:GCTT,GSM935120,GSM935120: Dre 48h control; Danio rerio; OTHER,GSM935120 1,GSM935120: Dre 48h control,1,,GEO Accession:GSM935120,OTHER,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>,SRP013309,,,Dre_48h_control.gz,fastq,75389652.0,2094157.0,GSM935120 r1,0:36,A:13252992;C:21927091;G:18790968;T:21232585;N:186016,36,,,,13252992,21927091,18790968,21232585,186016,SRX148958,SRS334487,SRA053074,GEO,"van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter",1,0.12359,,0.01182,,0.95929,,0.56028,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,bulk,bulk,,United Kingdom,2012-05-22,Hatching,Embryo,Whole Organism,All anatomical structures
49501,SRR7909906,SRX4746023,SRS3826020,SRP162761,PRJNA493632,Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq],GSE120578,Transcriptome Analysis,To characterize the distinct features of HSPCs and relevant niche cells  we performed RNA seq with sorted zebrafish HSPCs and niche cells  based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs  ECs and NCs from embryonic tails at 36 hpf  52 hpf  3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.,parent bioproject:PRJNA493631,pubmed:31042481;pubmed:33785593,,52 hpf CHT NC rep2,GSM3403645,,source name:zebrafish embryos|tissue:zebrafish embryos|cell type:double negative cells|Stage:52 hpf,52 hpf CHT NC rep2,"Reads quality were first checked by ""Fastqc"" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters  and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples  measured by FPKM",zebrafish embryos,,The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.,,tissue:zebrafish embryos|cell type:double negative cells|Stage:52 hpf,GSM3403645,GSM3403645: 52 hpf CHT NC rep2; Danio rerio; RNA Seq,GSM3403645,,1,The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.,GEO Accession:GSM3403645,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP162761,,,NC-2_HNJNLCCXX_L6_1.clean.fq.gz NC-2_HNJNLCCXX_L6_2.clean.fq.gz,fastq fastq,9365683800.0,31218946.0,GSM3403645 r1,0:150 1:150,A:2345549529;C:2328220975;G:2350758892;T:2339854432;N:1299972,150,150,,,2345549529,2328220975,2350758892,2339854432,1299972,SRX4746023,SRS3826020,SRA785160,GEO,"Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)",2,0.92542,0.92647,0.07392,0.07341,0.72681,0.7305,0.48431,0.49202,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2018-09-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
49502,SRR7909905,SRX4746022,SRS3826037,SRP162761,PRJNA493632,Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq],GSE120578,Transcriptome Analysis,To characterize the distinct features of HSPCs and relevant niche cells  we performed RNA seq with sorted zebrafish HSPCs and niche cells  based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs  ECs and NCs from embryonic tails at 36 hpf  52 hpf  3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.,parent bioproject:PRJNA493631,pubmed:31042481;pubmed:33785593,,52 hpf CHT NC rep1,GSM3403644,,source name:zebrafish embryos|tissue:zebrafish embryos|cell type:double negative cells|Stage:52 hpf,52 hpf CHT NC rep1,"Reads quality were first checked by ""Fastqc"" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters  and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples  measured by FPKM",zebrafish embryos,,The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.,,tissue:zebrafish embryos|cell type:double negative cells|Stage:52 hpf,GSM3403644,GSM3403644: 52 hpf CHT NC rep1; Danio rerio; RNA Seq,GSM3403644,,1,The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.,GEO Accession:GSM3403644,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP162761,,,NC1_HVL3KCCXX_L7_1.clean.fq.gz NC1_HVL3KCCXX_L7_2.clean.fq.gz,fastq fastq,8148991500.0,27163305.0,GSM3403644 r1,0:150 1:150,A:2084601119;C:1986552635;G:2011693786;T:2065591952;N:552008,150,150,,,2084601119,1986552635,2011693786,2065591952,552008,SRX4746022,SRS3826037,SRA785160,GEO,"Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)",2,0.92355,0.92768,0.0658,0.0663,0.72021,0.72474,0.47658,0.48053,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2018-09-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
56512,SRR10988549,SRX7649999,SRS6079496,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib3,GSM4289907,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib3,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289907,GSM4289907: head  2d rw440 sib3; Danio rerio; RNA Seq,GSM4289907,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289907,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib3_R2.fastq.gz 2d_rw440_sib3_R1.fastq.gz,fastq fastq,3140682329.0,10457484.0,GSM4289907 r1,0:150.21 1:150.12,A:760684292;C:777389008;G:783922642;T:818121129;N:565258,150,150,,,760684292,777389008,783922642,818121129,565258,SRX7649999,SRS6079496,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93527,0.95251,0.03293,0.02826,0.72032,0.73669,0.4787,0.47899,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56513,SRR10988548,SRX7649998,SRS6079495,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib2,GSM4289906,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib2,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289906,GSM4289906: head  2d rw440 sib2; Danio rerio; RNA Seq,GSM4289906,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289906,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib2_R1.fastq.gz 2d_rw440_sib2_R2.fastq.gz,fastq fastq,3194598681.0,10634398.0,GSM4289906 r1,0:150.24 1:150.17,A:771547062;C:789590364;G:796831526;T:835985747;N:643982,150,150,,,771547062,789590364,796831526,835985747,643982,SRX7649998,SRS6079495,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93377,0.95416,0.02628,0.02182,0.72989,0.74805,0.46631,0.47654,149,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56514,SRR10988547,SRX7649997,SRS6079494,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 sib1,GSM4289905,,source name:head|tissue:Head|age:2dpf,head  2d rw440 sib1,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf,GSM4289905,GSM4289905: head  2d rw440 sib1; Danio rerio; RNA Seq,GSM4289905,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289905,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_sib1_R1.fastq.gz 2d_rw440_sib1_R2.fastq.gz,fastq fastq,2654979688.0,8840507.0,GSM4289905 r1,0:150.19 1:150.13,A:624000299;C:675145222;G:678635011;T:676731946;N:467210,150,150,,,624000299,675145222,678635011,676731946,467210,SRX7649997,SRS6079494,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.9317,0.94861,0.06364,0.05753,0.72811,0.75055,0.50771,0.52256,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56515,SRR10988546,SRX7649996,SRS6079493,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut3,GSM4289904,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut3,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289904,GSM4289904: head  2d rw440 mut3; Danio rerio; RNA Seq,GSM4289904,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289904,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut3_R1.fastq.gz 2d_rw440_mut3_R2.fastq.gz,fastq fastq,3282506507.0,10958106.0,GSM4289904 r1,0:149.81 1:149.74,A:781014809;C:816143245;G:824711112;T:858035111;N:2602230,149,149,,,781014809,816143245,824711112,858035111,2602230,SRX7649996,SRS6079493,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93293,0.95901,0.02641,0.023,0.74408,0.76449,0.48032,0.475,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56516,SRR10988545,SRX7649995,SRS6079492,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut2,GSM4289903,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut2,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289903,GSM4289903: head  2d rw440 mut2; Danio rerio; RNA Seq,GSM4289903,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289903,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut2_R2.fastq.gz 2d_rw440_mut2_R1.fastq.gz,fastq fastq,2673347852.0,8908620.0,GSM4289903 r1,0:150.07 1:150.01,A:641733072;C:667262119;G:672992510;T:690242042;N:1118109,150,150,,,641733072,667262119,672992510,690242042,1118109,SRX7649995,SRS6079492,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93754,0.95755,0.03962,0.0352,0.72234,0.73963,0.47668,0.49072,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
56517,SRR10988544,SRX7649994,SRS6079491,SRP246053,PRJNA603897,Comparsion of transcriptome between slbp1 mutant and wildtype sibling,GSE144517,Transcriptome Analysis,"The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant ""slbp1"" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.",,,,head  2d rw440 mut1,GSM4289902,,source name:head|tissue:Head|age:2dpf / ,head  2d rw440 mut1,"Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 whole genome using hisat2  with parameters  k 3  p 36 Raw count data was obtained by featureCounts with parameters  p  T 36   t exon  g gene id  a ""GRCz11"" cut  f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file",head,,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:Head|age:2dpf / ,GSM4289902,GSM4289902: head  2d rw440 mut1; Danio rerio; RNA Seq,GSM4289902,,1,Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4289902,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP246053,,,2d_rw440_mut1_R1.fastq.gz 2d_rw440_mut1_R2.fastq.gz,fastq fastq,2609801785.0,8695280.0,GSM4289902 r1,0:150.10 1:150.04,A:629026157;C:649393814;G:654616712;T:676204104;N:560998,150,150,,,629026157,649393814,654616712,676204104,560998,SRX7649994,SRS6079491,SRA1034453,GEO,"Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University",2,0.93478,0.95296,0.02959,0.0259,0.72458,0.74209,0.4765,0.47804,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Japan,2020-01-30,Hatching,Embryo,Head,Nervous System
58969,SRR11575113,SRX8143233,SRS6506144,SRP257532,PRJNA626621,Identification of target genes in tie1 mutant zebrafish heart by transcriptomic analysis,GSE148957,Transcriptome Analysis,Purpose: identifying  with RNA seq  genes targets of Tie1 during the cardiac development in zebrafish.  Results: we identified several differential expressed genes  with an enrichment in ECM modulator genes. Overall design: Hearts were manually extracted at 48 hpf from tie1 mutants and wild type and heterozygous siblings.,,,,tie1 WT 2,GSM4486659,,source name:Tgkdrl:eGFP|tissue:Hearts|developmental stage:48 hpf|genotype:tie1 WT,tie1 WT 2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at http://www.bioinformatics.babraham.ac.uk/ projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides 6.  Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package 8.  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Tgkdrl:eGFP,,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,,tissue:Hearts|developmental stage:48 hpf|genotype:tie1 WT,GSM4486659,GSM4486659: tie1 WT 2; Danio rerio; RNA Seq,GSM4486659,,1,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,GEO Accession:GSM4486659,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP257532,,,Carlantoni_RNA_WT_2.fastq.gz,fastq,1305381389.0,17502572.0,GSM4486659 r1,0:74.58 1:0,A:237331428;C:438050630;G:373885000;T:256109188;N:5143,74,0,,,237331428,438050630,373885000,256109188,5143,SRX8143233,SRS6506144,SRA1067178,GEO,MPI for heart and lung research,1,0.9611,,0.16835,,0.89919,,0.79231,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,Germany,2020-04-20,Hatching,Embryo,Heart,Cardiovascular System
58970,SRR11575112,SRX8143232,SRS6506143,SRP257532,PRJNA626621,Identification of target genes in tie1 mutant zebrafish heart by transcriptomic analysis,GSE148957,Transcriptome Analysis,Purpose: identifying  with RNA seq  genes targets of Tie1 during the cardiac development in zebrafish.  Results: we identified several differential expressed genes  with an enrichment in ECM modulator genes. Overall design: Hearts were manually extracted at 48 hpf from tie1 mutants and wild type and heterozygous siblings.,,,,tie1 WT 1,GSM4486658,,source name:Tgkdrl:eGFP|tissue:Hearts|developmental stage:48 hpf|genotype:tie1 WT,tie1 WT 1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at http://www.bioinformatics.babraham.ac.uk/ projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides 6.  Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package 8.  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Tgkdrl:eGFP,,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,,tissue:Hearts|developmental stage:48 hpf|genotype:tie1 WT,GSM4486658,GSM4486658: tie1 WT 1; Danio rerio; RNA Seq,GSM4486658,,1,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,GEO Accession:GSM4486658,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP257532,,,Carlantoni_RNA_WT_1.fastq.gz,fastq,1494085887.0,20050038.0,GSM4486658 r1,0:74.52 1:0,A:282811923;C:486533537;G:414513849;T:310220539;N:6039,74,0,,,282811923,486533537,414513849,310220539,6039,SRX8143232,SRS6506143,SRA1067178,GEO,MPI for heart and lung research,1,0.9512,,0.17902,,0.89757,,0.79881,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,Germany,2020-04-20,Hatching,Embryo,Heart,Cardiovascular System
58971,SRR11575111,SRX8143231,SRS6506142,SRP257532,PRJNA626621,Identification of target genes in tie1 mutant zebrafish heart by transcriptomic analysis,GSE148957,Transcriptome Analysis,Purpose: identifying  with RNA seq  genes targets of Tie1 during the cardiac development in zebrafish.  Results: we identified several differential expressed genes  with an enrichment in ECM modulator genes. Overall design: Hearts were manually extracted at 48 hpf from tie1 mutants and wild type and heterozygous siblings.,,,,tie1 KO 2,GSM4486657,,source name:Tgkdrl:eGFP|tissue:Hearts|developmental stage:48 hpf|genotype:tie1 KO,tie1 KO 2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at http://www.bioinformatics.babraham.ac.uk/ projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides 6.  Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package 8.  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Tgkdrl:eGFP,,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,,tissue:Hearts|developmental stage:48 hpf|genotype:tie1 KO,GSM4486657,GSM4486657: tie1 KO 2; Danio rerio; RNA Seq,GSM4486657,,1,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,GEO Accession:GSM4486657,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP257532,,,Carlantoni_RNA_KO_2.fastq.gz,fastq,1398062637.0,18750921.0,GSM4486657 r1,0:74.56 1:0,A:245160828;C:482535020;G:414010795;T:256350606;N:5388,74,0,,,245160828,482535020,414010795,256350606,5388,SRX8143231,SRS6506142,SRA1067178,GEO,MPI for heart and lung research,1,0.96112,,0.17097,,0.9263,,0.81149,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,Germany,2020-04-20,Hatching,Embryo,Heart,Cardiovascular System
58972,SRR11575110,SRX8143230,SRS6506141,SRP257532,PRJNA626621,Identification of target genes in tie1 mutant zebrafish heart by transcriptomic analysis,GSE148957,Transcriptome Analysis,Purpose: identifying  with RNA seq  genes targets of Tie1 during the cardiac development in zebrafish.  Results: we identified several differential expressed genes  with an enrichment in ECM modulator genes. Overall design: Hearts were manually extracted at 48 hpf from tie1 mutants and wild type and heterozygous siblings.,,,,tie1 KO 1,GSM4486656,,source name:Tgkdrl:eGFP|tissue:Hearts|developmental stage:48 hpf|genotype:tie1 KO,tie1 KO 1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at http://www.bioinformatics.babraham.ac.uk/ projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides 6.  Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package 8.  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Tgkdrl:eGFP,,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,,tissue:Hearts|developmental stage:48 hpf|genotype:tie1 KO,GSM4486656,GSM4486656: tie1 KO 1; Danio rerio; RNA Seq,GSM4486656,,1,Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles  pooled in 1.5 ml tubes with TRIzol and frozen in  80°C. Total RNA was isolated using the miRNeasy micro kit Qiagen.  For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen.  Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 2 ng of total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit   Pico Input Mammalian Takara Clontech.,GEO Accession:GSM4486656,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP257532,,,Carlantoni_RNA_KO_1.fastq.gz,fastq,1236313899.0,16596670.0,GSM4486656 r1,0:74.49 1:0,A:227398977;C:410185357;G:353761139;T:244963695;N:4731,74,0,,,227398977,410185357,353761139,244963695,4731,SRX8143230,SRS6506141,SRA1067178,GEO,MPI for heart and lung research,1,0.95313,,0.17078,,0.90723,,0.82365,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,Germany,2020-04-20,Hatching,Embryo,Heart,Cardiovascular System
63643,SRR13979112,SRX10356673,SRS8474629,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep4,GSM5174052,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174052,GSM5174052: miRNA TiBP rep4; Danio rerio; miRNA Seq,GSM5174052,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174052,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s028-indexRPI28-CAAAAG-52_S28_L001_R1_001.fastq.gz,fastq,910334614.0,9013214.0,GSM5174052 r1,0:101 1:0,A:290447743;C:219962173;G:188092578;T:211816048;N:16072,101,0,,,290447743,219962173,188092578,211816048,16072,SRX10356673,SRS8474629,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00011,,0.0,,0.99967,,0.75,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63644,SRR13979111,SRX10356672,SRS8474628,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep3,GSM5174051,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174051,GSM5174051: miRNA TiBP rep3; Danio rerio; miRNA Seq,GSM5174051,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174051,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s027-indexRPI27-ATTCCT-51_S27_L001_R1_001.fastq.gz,fastq,1206610034.0,11946634.0,GSM5174051 r1,0:101 1:0,A:350061820;C:302802434;G:235521116;T:318199102;N:25562,101,0,,,350061820,302802434,235521116,318199102,25562,SRX10356672,SRS8474628,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99965,,0.79166,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63645,SRR13979110,SRX10356671,SRS8474626,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep2,GSM5174050,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174050,GSM5174050: miRNA TiBP rep2; Danio rerio; miRNA Seq,GSM5174050,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174050,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s026-indexRPI26-ATGAGC-50_S26_L001_R1_001.fastq.gz,fastq,464537279.0,4599379.0,GSM5174050 r1,0:101 1:0,A:139497834;C:112216637;G:99887123;T:112926329;N:9356,101,0,,,139497834,112216637,99887123,112926329,9356,SRX10356671,SRS8474626,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00022,,1e-05,,0.99955,,0.61538,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63646,SRR13979109,SRX10356670,SRS8474627,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TiBP rep1,GSM5174049,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TiBP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174049,GSM5174049: miRNA TiBP rep1; Danio rerio; miRNA Seq,GSM5174049,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174049,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s025-indexRPI25-ACTGAT-49_S25_L001_R1_001.fastq.gz,fastq,1146926508.0,11355708.0,GSM5174049 r1,0:101 1:0,A:344954395;C:275566512;G:235491109;T:290891698;N:22794,101,0,,,344954395,275566512,235491109,290891698,22794,SRX10356670,SRS8474627,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,1e-05,,0.99965,,0.71875,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63647,SRR13979108,SRX10356669,SRS8474625,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep4,GSM5174048,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174048,GSM5174048: miRNA TPP rep4; Danio rerio; miRNA Seq,GSM5174048,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174048,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s036-indexRPI36-CCAACA-60_S36_L001_R1_001.fastq.gz,fastq,927517340.0,9183340.0,GSM5174048 r1,0:101 1:0,A:288988916;C:242744912;G:181427113;T:214337769;N:18630,101,0,,,288988916,242744912,181427113,214337769,18630,SRX10356669,SRS8474625,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00023,,1e-05,,0.99955,,0.70731,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63648,SRR13979107,SRX10356668,SRS8474624,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep3,GSM5174047,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174047,GSM5174047: miRNA TPP rep3; Danio rerio; miRNA Seq,GSM5174047,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174047,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s035-indexRPI35-CATTTT-59_S35_L001_R1_001.fastq.gz,fastq,1013252907.0,10032207.0,GSM5174047 r1,0:101 1:0,A:295518831;C:243561888;G:197719671;T:276430583;N:21934,101,0,,,295518831,243561888,197719671,276430583,21934,SRX10356668,SRS8474624,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99973,,0.48,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63649,SRR13979106,SRX10356667,SRS8474623,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep2,GSM5174046,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174046,GSM5174046: miRNA TPP rep2; Danio rerio; miRNA Seq,GSM5174046,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174046,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s034-indexRPI34-CATGGC-58_S34_L001_R1_001.fastq.gz,fastq,907210381.0,8982281.0,GSM5174046 r1,0:101 1:0,A:265012714;C:227793861;G:194928689;T:219454152;N:20965,101,0,,,265012714,227793861,194928689,219454152,20965,SRX10356667,SRS8474623,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99965,,0.875,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63650,SRR13979105,SRX10356666,SRS8474622,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TPP rep1,GSM5174045,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174045,GSM5174045: miRNA TPP rep1; Danio rerio; miRNA Seq,GSM5174045,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174045,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s033-indexRPI33-CAGGCG-57_S33_L001_R1_001.fastq.gz,fastq,980681013.0,9709713.0,GSM5174045 r1,0:101 1:0,A:286952877;C:245397809;G:220787030;T:227522023;N:21274,101,0,,,286952877,245397809,220787030,227522023,21274,SRX10356666,SRS8474622,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,1e-05,,0.99961,,0.72222,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63651,SRR13979104,SRX10356665,SRS8474621,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep4,GSM5174044,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174044,GSM5174044: miRNA TBPH rep4; Danio rerio; miRNA Seq,GSM5174044,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174044,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s012-indexRPI12-CTTGTA-24_S12_L001_R1_001.fastq.gz,fastq,879997850.0,8712850.0,GSM5174044 r1,0:101 1:0,A:257202916;C:211754629;G:179803383;T:231218549;N:18373,101,0,,,257202916,211754629,179803383,231218549,18373,SRX10356665,SRS8474621,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00022,,0.0,,0.99961,,0.55,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63652,SRR13979103,SRX10356664,SRS8474620,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep3,GSM5174043,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174043,GSM5174043: miRNA TBPH rep3; Danio rerio; miRNA Seq,GSM5174043,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174043,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s011-indexRPI11-GGCTAC-23_S11_L001_R1_001.fastq.gz,fastq,883707883.0,8749583.0,GSM5174043 r1,0:101 1:0,A:256575313;C:222504855;G:189827000;T:214781797;N:18918,101,0,,,256575313,222504855,189827000,214781797,18918,SRX10356664,SRS8474620,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,0.0,,0.99961,,0.725,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63653,SRR13979102,SRX10356663,SRS8474619,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep2,GSM5174042,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174042,GSM5174042: miRNA TBPH rep2; Danio rerio; miRNA Seq,GSM5174042,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174042,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s010-indexRPI10-TAGCTT-22_S10_L001_R1_001.fastq.gz,fastq,727499667.0,7202967.0,GSM5174042 r1,0:101 1:0,A:212029291;C:175832603;G:148851978;T:190770471;N:15324,101,0,,,212029291,175832603,148851978,190770471,15324,SRX10356663,SRS8474619,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00025,,1e-05,,0.99951,,0.68181,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63654,SRR13979101,SRX10356662,SRS8474618,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBPH rep1,GSM5174041,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBPH rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174041,GSM5174041: miRNA TBPH rep1; Danio rerio; miRNA Seq,GSM5174041,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174041,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s009-indexRPI9-GATCAG-21_S9_L001_R1_001.fastq.gz,fastq,351322743.0,3478443.0,GSM5174041 r1,0:101 1:0,A:105338110;C:85172820;G:75749691;T:85054964;N:7158,101,0,,,105338110,85172820,75749691,85054964,7158,SRX10356662,SRS8474618,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00036,,1e-05,,0.99953,,0.52238,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63655,SRR13979100,SRX10356661,SRS8474616,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep4,GSM5174040,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174040,GSM5174040: miRNA TCEP rep4; Danio rerio; miRNA Seq,GSM5174040,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174040,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s044-indexRPI44-TATAAT-72_S44_L001_R1_001.fastq.gz,fastq,904258656.0,8953056.0,GSM5174040 r1,0:101 1:0,A:282578101;C:207780974;G:175938229;T:237943510;N:17842,101,0,,,282578101,207780974,175938229,237943510,17842,SRX10356661,SRS8474616,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.0002,,0.0,,0.99951,,0.72972,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63656,SRR13979099,SRX10356660,SRS8474615,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep3,GSM5174039,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174039,GSM5174039: miRNA TCEP rep3; Danio rerio; miRNA Seq,GSM5174039,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174039,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s043-indexRPI43-TACAGC-71_S43_L001_R1_001.fastq.gz,fastq,908098777.0,8991077.0,GSM5174039 r1,0:101 1:0,A:274350569;C:227463819;G:185316266;T:220948697;N:19426,101,0,,,274350569,227463819,185316266,220948697,19426,SRX10356660,SRS8474615,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00015,,0.0,,0.99965,,0.57142,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63657,SRR13979098,SRX10356659,SRS8474617,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep2,GSM5174038,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174038,GSM5174038: miRNA TCEP rep2; Danio rerio; miRNA Seq,GSM5174038,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174038,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s042-indexRPI42-TAATCG-70_S42_L001_R1_001.fastq.gz,fastq,738320403.0,7310103.0,GSM5174038 r1,0:101 1:0,A:221107544;C:178181142;G:152128298;T:186889068;N:14351,101,0,,,221107544,178181142,152128298,186889068,14351,SRX10356659,SRS8474617,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00017,,0.0,,0.99965,,0.59375,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63658,SRR13979097,SRX10356658,SRS8474612,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCEP rep1,GSM5174037,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCEP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174037,GSM5174037: miRNA TCEP rep1; Danio rerio; miRNA Seq,GSM5174037,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174037,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s041-indexRPI41-GACGAC-69_S41_L001_R1_001.fastq.gz,fastq,470221761.0,4655661.0,GSM5174037 r1,0:101 1:0,A:142688200;C:117856681;G:100380615;T:109286679;N:9586,101,0,,,142688200,117856681,100380615,109286679,9586,SRX10356658,SRS8474612,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00028,,1e-05,,0.99951,,0.66666,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63659,SRR13979096,SRX10356657,SRS8474613,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep4,GSM5174036,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174036,GSM5174036: miRNA TDBPP rep4; Danio rerio; miRNA Seq,GSM5174036,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174036,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s024-indexRPI24-GGTAGC-48_S24_L001_R1_001.fastq.gz,fastq,889897668.0,8810868.0,GSM5174036 r1,0:101 1:0,A:253810688;C:216798740;G:203615337;T:215653771;N:19132,101,0,,,253810688,216798740,203615337,215653771,19132,SRX10356657,SRS8474613,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,0.0,,0.99963,,0.41176,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63660,SRR13979095,SRX10356656,SRS8474614,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep3,GSM5174035,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174035,GSM5174035: miRNA TDBPP rep3; Danio rerio; miRNA Seq,GSM5174035,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174035,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s023-indexRPI23-GAGTGG-47_S23_L001_R1_001.fastq.gz,fastq,528666623.0,5234323.0,GSM5174035 r1,0:101 1:0,A:145917522;C:125201606;G:128827845;T:128709318;N:10332,101,0,,,145917522,125201606,128827845,128709318,10332,SRX10356656,SRS8474614,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,0.0,,0.99961,,0.56818,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63661,SRR13979094,SRX10356655,SRS8474609,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep2,GSM5174034,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174034,GSM5174034: miRNA TDBPP rep2; Danio rerio; miRNA Seq,GSM5174034,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174034,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s022-indexRPI22-CGTACG-46_S22_L001_R1_001.fastq.gz,fastq,906963537.0,8979837.0,GSM5174034 r1,0:101 1:0,A:246251307;C:236436405;G:206539134;T:217717657;N:19034,101,0,,,246251307,236436405,206539134,217717657,19034,SRX10356655,SRS8474609,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00015,,0.0,,0.99967,,0.65384,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63662,SRR13979093,SRX10356654,SRS8474611,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TDBPP rep1,GSM5174033,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TDBPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174033,GSM5174033: miRNA TDBPP rep1; Danio rerio; miRNA Seq,GSM5174033,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174033,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s021-indexRPI21-GTTTCG-45_S21_L001_R1_001.fastq.gz,fastq,556898547.0,5513847.0,GSM5174033 r1,0:101 1:0,A:149304325;C:137357612;G:124103413;T:146121425;N:11772,101,0,,,149304325,137357612,124103413,146121425,11772,SRX10356654,SRS8474611,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,0.0,,0.99957,,0.7027,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63663,SRR13979092,SRX10356653,SRS8474610,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep4,GSM5174032,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174032,GSM5174032: miRNA TCPP rep4; Danio rerio; miRNA Seq,GSM5174032,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174032,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s016-indexRPI16-CCGTCC-28_S16_L001_R1_001.fastq.gz,fastq,885697179.0,8769279.0,GSM5174032 r1,0:101 1:0,A:247836719;C:241737695;G:181087463;T:215012979;N:22323,101,0,,,247836719,241737695,181087463,215012979,22323,SRX10356653,SRS8474610,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,0.0,,0.99967,,0.68571,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63664,SRR13979091,SRX10356652,SRS8474608,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep3,GSM5174031,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174031,GSM5174031: miRNA TCPP rep3; Danio rerio; miRNA Seq,GSM5174031,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174031,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s015-indexRPI15-ATGTCA-27_S15_L001_R1_001.fastq.gz,fastq,566510010.0,5609010.0,GSM5174031 r1,0:101 1:0,A:170383116;C:137048514;G:115945259;T:143122249;N:10872,101,0,,,170383116,137048514,115945259,143122249,10872,SRX10356652,SRS8474608,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00025,,0.0,,0.99967,,0.54347,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63665,SRR13979090,SRX10356651,SRS8474607,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep2,GSM5174030,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174030,GSM5174030: miRNA TCPP rep2; Danio rerio; miRNA Seq,GSM5174030,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174030,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s014-indexRPI14-AGTTCC-26_S14_L001_R1_001.fastq.gz,fastq,892405902.0,8835702.0,GSM5174030 r1,0:101 1:0,A:259754435;C:224608997;G:182748088;T:225275385;N:18997,101,0,,,259754435,224608997,182748088,225275385,18997,SRX10356651,SRS8474607,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00022,,0.0,,0.99951,,0.64285,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63666,SRR13979089,SRX10356650,SRS8474606,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TCPP rep1,GSM5174029,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TCPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174029,GSM5174029: miRNA TCPP rep1; Danio rerio; miRNA Seq,GSM5174029,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174029,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s013-indexRPI13-AGTCAA-25_S13_L001_R1_001.fastq.gz,fastq,1059166295.0,10486795.0,GSM5174029 r1,0:101 1:0,A:329962449;C:255719926;G:216763563;T:256700660;N:19697,101,0,,,329962449,255719926,216763563,256700660,19697,SRX10356650,SRS8474606,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,1e-05,,0.99969,,0.63636,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63667,SRR13979088,SRX10356649,SRS8474605,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep4,GSM5174028,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174028,GSM5174028: miRNA TBBPA rep4; Danio rerio; miRNA Seq,GSM5174028,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174028,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s008-indexRPI8-ACTTGA-20_S8_L001_R1_001.fastq.gz,fastq,868526270.0,8599270.0,GSM5174028 r1,0:101 1:0,A:259616680;C:210636450;G:178110756;T:220145615;N:16769,101,0,,,259616680,210636450,178110756,220145615,16769,SRX10356649,SRS8474605,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00023,,0.0,,0.99961,,0.67441,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63668,SRR13979087,SRX10356648,SRS8474604,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep3,GSM5174027,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174027,GSM5174027: miRNA TBBPA rep3; Danio rerio; miRNA Seq,GSM5174027,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174027,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s007-indexRPI7-CAGATC-19_S7_L001_R1_001.fastq.gz,fastq,493578011.0,4886911.0,GSM5174027 r1,0:101 1:0,A:147046152;C:124953541;G:102431606;T:119137120;N:9592,101,0,,,147046152,124953541,102431606,119137120,9592,SRX10356648,SRS8474604,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,1e-05,,0.99947,,0.76744,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63669,SRR13979086,SRX10356647,SRS8474603,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep2,GSM5174026,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174026,GSM5174026: miRNA TBBPA rep2; Danio rerio; miRNA Seq,GSM5174026,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174026,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s006-indexRPI6-GCCAAT-18_S6_L001_R1_001.fastq.gz,fastq,910368853.0,9013553.0,GSM5174026 r1,0:101 1:0,A:270122236;C:230334670;G:190520709;T:219373774;N:17464,101,0,,,270122236,230334670,190520709,219373774,17464,SRX10356647,SRS8474603,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00023,,0.0,,0.99949,,0.72727,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63670,SRR13979085,SRX10356646,SRS8474602,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA rep1,GSM5174025,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA TBBPA rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174025,GSM5174025: miRNA TBBPA rep1; Danio rerio; miRNA Seq,GSM5174025,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174025,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s005-indexRPI5-ACAGTG-17_S5_L001_R1_001.fastq.gz,fastq,894131992.0,8852792.0,GSM5174025 r1,0:101 1:0,A:261443048;C:220215927;G:200185007;T:212270956;N:17054,101,0,,,261443048,220215927,200185007,212270956,17054,SRX10356646,SRS8474602,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00021,,1e-05,,0.99953,,0.7027,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63671,SRR13979084,SRX10356645,SRS8474601,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep4,GSM5174024,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174024,GSM5174024: miRNA TBBPA DBPE rep4; Danio rerio; miRNA Seq,GSM5174024,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174024,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s040-indexRPI40-CTCAGA-68_S40_L001_R1_001.fastq.gz,fastq,567614950.0,5619950.0,GSM5174024 r1,0:101 1:0,A:171789620;C:142600627;G:115292068;T:137921194;N:11441,101,0,,,171789620,142600627,115292068,137921194,11441,SRX10356645,SRS8474601,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00014,,0.0,,0.99965,,0.55555,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63672,SRR13979083,SRX10356644,SRS8474600,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep3,GSM5174023,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174023,GSM5174023: miRNA TBBPA DBPE rep3; Danio rerio; miRNA Seq,GSM5174023,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174023,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s039-indexRPI39-CTATAC-67_S39_L001_R1_001.fastq.gz,fastq,883651020.0,8749020.0,GSM5174023 r1,0:101 1:0,A:267266527;C:221471697;G:172032269;T:222861646;N:18881,101,0,,,267266527,221471697,172032269,222861646,18881,SRX10356644,SRS8474600,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,1e-05,,0.99959,,0.65116,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63673,SRR13979082,SRX10356643,SRS8474599,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep2,GSM5174022,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174022,GSM5174022: miRNA TBBPA DBPE rep2; Danio rerio; miRNA Seq,GSM5174022,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174022,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s038-indexRPI38-CTAGCT-66_S38_L001_R1_001.fastq.gz,fastq,311086666.0,3080066.0,GSM5174022 r1,0:101 1:0,A:90852851;C:77957592;G:63570096;T:78699630;N:6497,101,0,,,90852851,77957592,63570096,78699630,6497,SRX10356643,SRS8474599,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00036,,1e-05,,0.99947,,0.6875,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63674,SRR13979081,SRX10356642,SRS8474598,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA TBBPA DBPE rep1,GSM5174021,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,miRNA TBBPA DBPE rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf DBPE,GSM5174021,GSM5174021: miRNA TBBPA DBPE rep1; Danio rerio; miRNA Seq,GSM5174021,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174021,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s037-indexRPI37-CGGAAT-65_S37_L001_R1_001.fastq.gz,fastq,1002314506.0,9923906.0,GSM5174021 r1,0:101 1:0,A:303735625;C:240217618;G:214324562;T:244016797;N:19904,101,0,,,303735625,240217618,214324562,244016797,19904,SRX10356642,SRS8474598,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,1e-05,,0.99953,,0.66666,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63675,SRR13979080,SRX10356641,SRS8474597,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep4,GSM5174020,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174020,GSM5174020: miRNA IPP rep4; Danio rerio; miRNA Seq,GSM5174020,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174020,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s032-indexRPI32-CACTCA-56_S32_L001_R1_001.fastq.gz,fastq,1129258881.0,11180781.0,GSM5174020 r1,0:101 1:0,A:335239774;C:296599595;G:223965990;T:273431685;N:21837,101,0,,,335239774,296599595,223965990,273431685,21837,SRX10356641,SRS8474597,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99959,,0.75,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63676,SRR13979079,SRX10356640,SRS8474596,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep3,GSM5174019,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174019,GSM5174019: miRNA IPP rep3; Danio rerio; miRNA Seq,GSM5174019,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174019,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s031-indexRPI31-CACGAT-55_S31_L001_R1_001.fastq.gz,fastq,1364695941.0,13511841.0,GSM5174019 r1,0:101 1:0,A:408343873;C:341704999;G:281119661;T:333499060;N:28348,101,0,,,408343873,341704999,281119661,333499060,28348,SRX10356640,SRS8474596,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00016,,0.0,,0.99961,,0.68965,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63677,SRR13979078,SRX10356639,SRS8474595,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep2,GSM5174018,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174018,GSM5174018: miRNA IPP rep2; Danio rerio; miRNA Seq,GSM5174018,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174018,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s030-indexRPI30-CACCGG-54_S30_L001_R1_001.fastq.gz,fastq,1118435923.0,11073623.0,GSM5174018 r1,0:101 1:0,A:322914077;C:292720303;G:241919484;T:260855307;N:26752,101,0,,,322914077,292720303,241919484,260855307,26752,SRX10356639,SRS8474595,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.0002,,1e-05,,0.99959,,0.74285,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63678,SRR13979077,SRX10356638,SRS8474594,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA IPP rep1,GSM5174017,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA IPP rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174017,GSM5174017: miRNA IPP rep1; Danio rerio; miRNA Seq,GSM5174017,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174017,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s029-indexRPI29-CAACTA-53_S29_L001_R1_001.fastq.gz,fastq,965915217.0,9563517.0,GSM5174017 r1,0:101 1:0,A:298517953;C:241792467;G:190277966;T:235308237;N:18594,101,0,,,298517953,241792467,190277966,235308237,18594,SRX10356638,SRS8474594,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00011,,0.0,,0.99973,,0.55,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63679,SRR13979076,SRX10356637,SRS8474593,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep4,GSM5174016,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174016,GSM5174016: miRNA BDE 47 rep4; Danio rerio; miRNA Seq,GSM5174016,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174016,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s020-indexRPI20-GTGGCC-44_S20_L001_R1_001.fastq.gz,fastq,990919989.0,9811089.0,GSM5174016 r1,0:101 1:0,A:281268229;C:247800394;G:221010761;T:240816791;N:23814,101,0,,,281268229,247800394,221010761,240816791,23814,SRX10356637,SRS8474593,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00016,,0.0,,0.99965,,0.7,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63680,SRR13979075,SRX10356636,SRS8474592,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep3,GSM5174015,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174015,GSM5174015: miRNA BDE 47 rep3; Danio rerio; miRNA Seq,GSM5174015,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174015,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s019-indexRPI19-GTGAAA-43_S19_L001_R1_001.fastq.gz,fastq,936520278.0,9272478.0,GSM5174015 r1,0:101 1:0,A:292610982;C:215924738;G:200657250;T:227310895;N:16413,101,0,,,292610982,215924738,200657250,227310895,16413,SRX10356636,SRS8474592,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00017,,0.0,,0.99961,,0.6,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63681,SRR13979074,SRX10356635,SRS8474591,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep2,GSM5174014,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174014,GSM5174014: miRNA BDE 47 rep2; Danio rerio; miRNA Seq,GSM5174014,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174014,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s018-indexRPI18-GTCCGC-42_S18_L001_R1_001.fastq.gz,fastq,923871038.0,9147238.0,GSM5174014 r1,0:101 1:0,A:261826604;C:240583077;G:197471686;T:223966265;N:23406,101,0,,,261826604,240583077,197471686,223966265,23406,SRX10356635,SRS8474591,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00019,,0.0,,0.99963,,0.70588,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63682,SRR13979073,SRX10356634,SRS8474588,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA BDE 47 rep1,GSM5174013,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA BDE 47 rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174013,GSM5174013: miRNA BDE 47 rep1; Danio rerio; miRNA Seq,GSM5174013,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174013,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s017-indexRPI17-GTAGAG-41_S17_L001_R1_001.fastq.gz,fastq,963214780.0,9536780.0,GSM5174013 r1,0:101 1:0,A:290268878;C:222146596;G:216903245;T:233878186;N:17875,101,0,,,290268878,222146596,216903245,233878186,17875,SRX10356634,SRS8474588,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00013,,0.0,,0.99971,,0.58333,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63683,SRR13979072,SRX10356633,SRS8474589,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep4,GSM5174012,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep4,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174012,GSM5174012: miRNA Control rep4; Danio rerio; miRNA Seq,GSM5174012,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174012,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s004-indexRPI4-TGACCA-4_S4_L001_R1_001.fastq.gz,fastq,776677274.0,7689874.0,GSM5174012 r1,0:101 1:0,A:233505881;C:196049592;G:158864473;T:188241779;N:15549,101,0,,,233505881,196049592,158864473,188241779,15549,SRX10356633,SRS8474589,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00024,,0.0,,0.99949,,0.76086,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63684,SRR13979071,SRX10356632,SRS8474590,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep3,GSM5174011,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep3,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174011,GSM5174011: miRNA Control rep3; Danio rerio; miRNA Seq,GSM5174011,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174011,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s003-indexRPI3-TTAGGC-3_S3_L001_R1_001.fastq.gz,fastq,489457615.0,4846115.0,GSM5174011 r1,0:101 1:0,A:141598763;C:118796680;G:105152559;T:123899061;N:10552,101,0,,,141598763,118796680,105152559,123899061,10552,SRX10356632,SRS8474590,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00037,,0.0,,0.99947,,0.66666,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63685,SRR13979070,SRX10356631,SRS8474586,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep2,GSM5174010,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep2,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174010,GSM5174010: miRNA Control rep2; Danio rerio; miRNA Seq,GSM5174010,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174010,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s002-indexRPI2-CGATGT-2_S2_L001_R1_001.fastq.gz,fastq,777242066.0,7695466.0,GSM5174010 r1,0:101 1:0,A:226389551;C:187485077;G:166405949;T:196945091;N:16398,101,0,,,226389551,187485077,166405949,196945091,16398,SRX10356631,SRS8474586,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00026,,0.0,,0.99957,,0.62,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63686,SRR13979069,SRX10356630,SRS8474585,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,miRNA Control rep1,GSM5174009,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,miRNA Control rep1,For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample,zebrafish whole embryos,Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,,strain:5D|developmental stage:48 hpf,GSM5174009,GSM5174009: miRNA Control rep1; Danio rerio; miRNA Seq,GSM5174009,,1,FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA,GEO Accession:GSM5174009,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,miRNA_lane1-s001-indexRPI1-ATCACG-1_S1_L001_R1_001.fastq.gz,fastq,370858163.0,3671863.0,GSM5174009 r1,0:101 1:0,A:112058381;C:93306905;G:75506546;T:89979021;N:7310,101,0,,,112058381,93306905,75506546,89979021,7310,SRX10356630,SRS8474585,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.00033,,1e-05,,0.99949,,0.64516,,101,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63687,SRR13979068,SRX10356629,SRS8474587,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TCEP rep4,GSM5174008,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5174008,GSM5174008: mRNA TCEP rep4; Danio rerio; RNA Seq,GSM5174008,,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:GSM5174008,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane2-s030-indexRPI44-TATAAT-72_S30_L002_R1_001.fastq.gz,fastq,2775203361.0,27477261.0,GSM5174008 r1,0:101 1:0,A:794097422;C:551158157;G:572886431;T:856930579;N:130772,101,0,,,794097422,551158157,572886431,856930579,130772,SRX10356629,SRS8474587,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.89782,,0.19016,,0.68909,,0.44622,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63688,SRR13979067,SRX10356628,SRS8474584,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TCEP rep3,GSM5174007,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5174007,GSM5174007: mRNA TCEP rep3; Danio rerio; RNA Seq,GSM5174007,,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:GSM5174007,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane3-s044-indexRPI43-TACAGC-71_S44_L003_R1_001.fastq.gz,fastq,2685409412.0,26588212.0,GSM5174007 r1,0:101 1:0,A:767385640;C:533789382;G:554165307;T:829853043;N:216040,101,0,,,767385640,533789382,554165307,829853043,216040,SRX10356628,SRS8474584,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.89482,,0.1927,,0.69124,,0.44704,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63689,SRR13979066,SRX10356627,SRS8474582,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TCEP rep2,GSM5174006,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5174006,GSM5174006: mRNA TCEP rep2; Danio rerio; RNA Seq,GSM5174006,,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:GSM5174006,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane2-s029-indexRPI42-TAATCG-70_S29_L002_R1_001.fastq.gz,fastq,2421794766.0,23978166.0,GSM5174006 r1,0:101 1:0,A:664904264;C:489032543;G:522221823;T:745520532;N:115604,101,0,,,664904264,489032543,522221823,745520532,115604,SRX10356627,SRS8474582,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9046,,0.14487,,0.70737,,0.4585,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63690,SRR13979065,SRX10356626,SRS8474583,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TCEP rep1,GSM5174005,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5174005,GSM5174005: mRNA TCEP rep1; Danio rerio; RNA Seq,GSM5174005,,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:GSM5174005,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane1-s015-indexRPI41-GACGAC-69_S15_L001_R1_001.fastq.gz,fastq,3356096175.0,33228675.0,GSM5174005 r1,0:101 1:0,A:951034928;C:660595103;G:687014918;T:1057268653;N:182573,101,0,,,951034928,660595103,687014918,1057268653,182573,SRX10356626,SRS8474583,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.87794,,0.1917,,0.69921,,0.46119,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63691,SRR13979064,SRX10356625,SRS8474579,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TBBPA DBPE rep4,GSM5174004,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,mRNA 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,GSM5174004,GSM5174004: mRNA TBBPA DBPE rep4; Danio rerio; RNA Seq,GSM5174004,,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:GSM5174004,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane1-s014-indexRPI40-CTCAGA-68_S14_L001_R1_001.fastq.gz,fastq,3313329341.0,32805241.0,GSM5174004 r1,0:101 1:0,A:939650473;C:649504596;G:673233880;T:1050760098;N:180294,101,0,,,939650473,649504596,673233880,1050760098,180294,SRX10356625,SRS8474579,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.87508,,0.18422,,0.70153,,0.43726,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63692,SRR13979063,SRX10356624,SRS8474580,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TBBPA DBPE rep3,GSM5174003,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,mRNA 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,GSM5174003,GSM5174003: mRNA TBBPA DBPE rep3; Danio rerio; RNA Seq,GSM5174003,,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:GSM5174003,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane3-s043-indexRPI39-CTATAC-67_S43_L003_R1_001.fastq.gz,fastq,3069748449.0,30393549.0,GSM5174003 r1,0:101 1:0,A:861114226;C:610893266;G:632664072;T:964829389;N:247496,101,0,,,861114226,610893266,632664072,964829389,247496,SRX10356624,SRS8474580,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.88344,,0.16663,,0.69873,,0.44998,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63693,SRR13979062,SRX10356623,SRS8474581,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TBBPA DBPE rep2,GSM5174002,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,mRNA 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,GSM5174002,GSM5174002: mRNA TBBPA DBPE rep2; Danio rerio; RNA Seq,GSM5174002,,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:GSM5174002,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane2-s028-indexRPI38-CTAGCT-66_S28_L002_R1_001.fastq.gz,fastq,2886797857.0,28582157.0,GSM5174002 r1,0:101 1:0,A:816680168;C:572200265;G:592910784;T:904871068;N:135572,101,0,,,816680168,572200265,592910784,904871068,135572,SRX10356623,SRS8474581,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.87966,,0.19145,,0.69684,,0.45927,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63694,SRR13979061,SRX10356622,SRS8474578,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TBBPA DBPE rep1,GSM5174001,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE,mRNA 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,GSM5174001,GSM5174001: mRNA TBBPA DBPE rep1; Danio rerio; RNA Seq,GSM5174001,,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:GSM5174001,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane1-s013-indexRPI37-CGGAAT-65_S13_L001_R1_001.fastq.gz,fastq,3049262316.0,30190716.0,GSM5174001 r1,0:101 1:0,A:863672217;C:608308405;G:631170738;T:945941282;N:169674,101,0,,,863672217,608308405,631170738,945941282,169674,SRX10356622,SRS8474578,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.8878,,0.1776,,0.69463,,0.44452,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63695,SRR13979060,SRX10356621,SRS8474577,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TPP rep4,GSM5174000,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5174000,GSM5174000: mRNA TPP rep4; Danio rerio; RNA Seq,GSM5174000,,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:GSM5174000,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane3-s042-indexRPI36-CCAACA-60_S42_L003_R1_001.fastq.gz,fastq,2581315984.0,25557584.0,GSM5174000 r1,0:101 1:0,A:728582484;C:518486393;G:540611903;T:793422892;N:212312,101,0,,,728582484,518486393,540611903,793422892,212312,SRX10356621,SRS8474577,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.86798,,0.17111,,0.69643,,0.46497,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63696,SRR13979059,SRX10356620,SRS8474576,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TPP rep3,GSM5173999,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5173999,GSM5173999: mRNA TPP rep3; Danio rerio; RNA Seq,GSM5173999,,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:GSM5173999,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane3-s041-indexRPI35-CATTTT-59_S41_L003_R1_001.fastq.gz,fastq,2962827425.0,29334925.0,GSM5173999 r1,0:101 1:0,A:836495993;C:594706287;G:619357498;T:912025040;N:242607,101,0,,,836495993,594706287,619357498,912025040,242607,SRX10356620,SRS8474576,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.86734,,0.16245,,0.69585,,0.45295,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63697,SRR13979058,SRX10356619,SRS8474575,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TPP rep2,GSM5173998,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5173998,GSM5173998: mRNA TPP rep2; Danio rerio; RNA Seq,GSM5173998,,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:GSM5173998,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane2-s027-indexRPI34-CATGGC-58_S27_L002_R1_001.fastq.gz,fastq,2652288583.0,26260283.0,GSM5173998 r1,0:101 1:0,A:752034974;C:528422008;G:551052569;T:820652705;N:126327,101,0,,,752034974,528422008,551052569,820652705,126327,SRX10356619,SRS8474575,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.86464,,0.17543,,0.69613,,0.45735,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures
63698,SRR13979057,SRX10356618,SRS8474574,SRP310924,PRJNA714931,Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks,GSE169013,Transcriptome Analysis,Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf,,pubmed:33898466,,mRNA TPP rep1,GSM5173997,,tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf,mRNA 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,GSM5173997,GSM5173997: mRNA TPP rep1; Danio rerio; RNA Seq,GSM5173997,,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:GSM5173997,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP310924,,,mRNA_lane1-s012-indexRPI33-CAGGCG-57_S12_L001_R1_001.fastq.gz,fastq,3128270879.0,30972979.0,GSM5173997 r1,0:101 1:0,A:867362474;C:636617526;G:669028543;T:955092681;N:169655,101,0,,,867362474,636617526,669028543,955092681,169655,SRX10356618,SRS8474574,SRA1207022,GEO,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.88688,,0.13909,,0.70005,,0.45763,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2021-03-16,Hatching,Embryo,Whole Organism,All anatomical structures