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
10008,ERR4648708,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L001_R1_001.fastq.gz 15S6_S11_L001_R2_001.fastq.gz,fastq fastq,1591537736.0,10470643.0,E MTAB 9615:15S6 S11 L001 R,0:76 1:76,A:429238832;C:363616036;G:370142973;T:428278902;N:260993,76,76,,,429238832,363616036,370142973,428278902,260993,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94838,0.95275,0.11825,0.11227,0.67263,0.67535,0.47339,0.48683,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10009,ERR4648709,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L002_R1_001.fastq.gz 15S6_S11_L002_R2_001.fastq.gz,fastq fastq,1559456464.0,10259582.0,E MTAB 9615:15S6 S11 L002 R,0:76 1:76,A:420535603;C:356234776;G:362907355;T:419528118;N:250612,76,76,,,420535603,356234776,362907355,419528118,250612,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94922,0.95244,0.11903,0.11395,0.66931,0.67233,0.46849,0.48097,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10010,ERR4648710,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L003_R1_001.fastq.gz 15S6_S11_L003_R2_001.fastq.gz,fastq fastq,1611815600.0,10604050.0,E MTAB 9615:15S6 S11 L003 R,0:76 1:76,A:434815382;C:368453005;G:374802612;T:433582623;N:161978,76,76,,,434815382,368453005,374802612,433582623,161978,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94878,0.9521,0.11889,0.11284,0.67302,0.67521,0.47879,0.48281,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10011,ERR4648711,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L004_R1_001.fastq.gz 15S6_S11_L004_R2_001.fastq.gz,fastq fastq,1587249512.0,10442431.0,E MTAB 9615:15S6 S11 L004 R,0:76 1:76,A:428113406;C:362725542;G:369262476;T:427024700;N:123388,76,76,,,428113406,362725542,369262476,427024700,123388,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94868,0.95237,0.11954,0.1137,0.66888,0.67411,0.48327,0.48573,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10012,ERR4648704,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L001_R1_001.fastq.gz 15S5_S7_L001_R2_001.fastq.gz,fastq fastq,1695774928.0,11156414.0,E MTAB 9615:15S5 S7 L001 R,0:76 1:76,A:456096603;C:390987096;G:394091205;T:454321430;N:278594,76,76,,,456096603,390987096,394091205,454321430,278594,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94681,0.9507,0.14362,0.13726,0.67931,0.68087,0.49708,0.49164,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10013,ERR4648705,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L002_R1_001.fastq.gz 15S5_S7_L002_R2_001.fastq.gz,fastq fastq,1652445504.0,10871352.0,E MTAB 9615:15S5 S7 L002 R,0:76 1:76,A:444752710;C:381030057;G:383777650;T:442619007;N:266080,76,76,,,444752710,381030057,383777650,442619007,266080,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94649,0.94993,0.14201,0.1357,0.68124,0.68471,0.49354,0.48934,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10014,ERR4648706,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L003_R1_001.fastq.gz 15S5_S7_L003_R2_001.fastq.gz,fastq fastq,1721026536.0,11322543.0,E MTAB 9615:15S5 S7 L003 R,0:76 1:76,A:463210590;C:396958291;G:399739948;T:460942070;N:175637,76,76,,,463210590,396958291,399739948,460942070,175637,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94689,0.95134,0.14445,0.13799,0.68083,0.68308,0.4907,0.49184,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10015,ERR4648707,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L004_R1_001.fastq.gz 15S5_S7_L004_R2_001.fastq.gz,fastq fastq,1681600624.0,11063162.0,E MTAB 9615:15S5 S7 L004 R,0:76 1:76,A:452919887;C:387692803;G:390415798;T:450439351;N:132785,76,76,,,452919887,387692803,390415798,450439351,132785,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94692,0.95086,0.14315,0.13615,0.67992,0.68272,0.49657,0.49082,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10016,ERR4648700,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L001_R1_001.fastq.gz 15S1_S3_L001_R2_001.fastq.gz,fastq fastq,1684976544.0,11085372.0,E MTAB 9615:15S1 S3 L001 R,0:76 1:76,A:459213104;C:380435364;G:388061620;T:456986886;N:279570,76,76,,,459213104,380435364,388061620,456986886,279570,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94815,0.95291,0.11703,0.10838,0.69106,0.69256,0.48318,0.48685,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10017,ERR4648701,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L002_R1_001.fastq.gz 15S1_S3_L002_R2_001.fastq.gz,fastq fastq,1643737728.0,10814064.0,E MTAB 9615:15S1 S3 L002 R,0:76 1:76,A:448110182;C:371404635;G:378168271;T:445793393;N:261247,76,76,,,448110182,371404635,378168271,445793393,261247,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94922,0.95393,0.11448,0.10652,0.69134,0.69301,0.4816,0.48594,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10018,ERR4648702,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L003_R1_001.fastq.gz 15S1_S3_L003_R2_001.fastq.gz,fastq fastq,1703808888.0,11209269.0,E MTAB 9615:15S1 S3 L003 R,0:76 1:76,A:464594650;C:384747658;G:392231421;T:462069215;N:165944,76,76,,,464594650,384747658,392231421,462069215,165944,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94969,0.95388,0.11731,0.10782,0.6914,0.69325,0.48074,0.48209,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10019,ERR4648703,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L004_R1_001.fastq.gz 15S1_S3_L004_R2_001.fastq.gz,fastq fastq,1668108648.0,10974399.0,E MTAB 9615:15S1 S3 L004 R,0:76 1:76,A:455048996;C:376727183;G:383710020;T:452489191;N:133258,76,76,,,455048996,376727183,383710020,452489191,133258,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94927,0.95254,0.11691,0.10738,0.68956,0.69244,0.48172,0.48334,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10020,ERR4648696,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L001_R1_001.fastq.gz 15K6_S12_L001_R2_001.fastq.gz,fastq fastq,1609873040.0,10591270.0,E MTAB 9615:15K6 S12 L001 R,0:76 1:76,A:437147858;C:366192064;G:371108418;T:435155810;N:268890,76,76,,,437147858,366192064,371108418,435155810,268890,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94722,0.95179,0.13705,0.12981,0.67679,0.67866,0.48396,0.49346,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10021,ERR4648697,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L002_R1_001.fastq.gz 15K6_S12_L002_R2_001.fastq.gz,fastq fastq,1575514808.0,10365229.0,E MTAB 9615:15K6 S12 L002 R,0:76 1:76,A:428185491;C:358401918;G:362831429;T:425840762;N:255208,76,76,,,428185491,358401918,362831429,425840762,255208,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94785,0.9528,0.13846,0.13087,0.67592,0.67856,0.49265,0.48858,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10022,ERR4648698,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L003_R1_001.fastq.gz 15K6_S12_L003_R2_001.fastq.gz,fastq fastq,1630087216.0,10724258.0,E MTAB 9615:15K6 S12 L003 R,0:76 1:76,A:442997697;C:370859421;G:375516402;T:440546052;N:167644,76,76,,,442997697,370859421,375516402,440546052,167644,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94716,0.95256,0.13708,0.12903,0.67608,0.6804,0.48953,0.49399,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10023,ERR4648699,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L004_R1_001.fastq.gz 15K6_S12_L004_R2_001.fastq.gz,fastq fastq,1598521832.0,10516591.0,E MTAB 9615:15K6 S12 L004 R,0:76 1:76,A:434619516;C:363630314;G:368039060;T:432106642;N:126300,76,76,,,434619516,363630314,368039060,432106642,126300,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9476,0.95293,0.1363,0.12951,0.67677,0.67831,0.4896,0.48586,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10024,ERR4648692,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L001_R1_001.fastq.gz 15K5_S8_L001_R2_001.fastq.gz,fastq fastq,1615900448.0,10630924.0,E MTAB 9615:15K5 S8 L001 R,0:76 1:76,A:434660709;C:371711237;G:375977073;T:433284563;N:266866,76,76,,,434660709,371711237,375977073,433284563,266866,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94975,0.95448,0.13643,0.13022,0.68243,0.68266,0.48919,0.49247,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10025,ERR4648693,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L002_R1_001.fastq.gz 15K5_S8_L002_R2_001.fastq.gz,fastq fastq,1578139392.0,10382496.0,E MTAB 9615:15K5 S8 L002 R,0:76 1:76,A:424647045;C:363127751;G:366920105;T:423189068;N:255423,76,76,,,424647045,363127751,366920105,423189068,255423,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94906,0.95028,0.13531,0.12984,0.68045,0.68237,0.48576,0.48791,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10026,ERR4648694,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L003_R1_001.fastq.gz 15K5_S8_L003_R2_001.fastq.gz,fastq fastq,1639204480.0,10784240.0,E MTAB 9615:15K5 S8 L003 R,0:76 1:76,A:441158676;C:377209170;G:381225501;T:439441707;N:169426,76,76,,,441158676,377209170,381225501,439441707,169426,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94969,0.95069,0.13506,0.12904,0.68045,0.68318,0.48642,0.48116,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10027,ERR4648695,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L004_R1_001.fastq.gz 15K5_S8_L004_R2_001.fastq.gz,fastq fastq,1605273824.0,10561012.0,E MTAB 9615:15K5 S8 L004 R,0:76 1:76,A:432120953;C:369415812;G:373183577;T:430423263;N:130219,76,76,,,432120953,369415812,373183577,430423263,130219,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95,0.95371,0.13552,0.12855,0.68225,0.68501,0.48758,0.48873,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10028,ERR4648688,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L001_R1_001.fastq.gz 15K1_S4_L001_R2_001.fastq.gz,fastq fastq,1723024576.0,11335688.0,E MTAB 9615:15K1 S4 L001 R,0:76 1:76,A:478023461;C:380533603;G:386774939;T:477400237;N:292336,76,76,,,478023461,380533603,386774939,477400237,292336,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94662,0.95081,0.13443,0.12127,0.68582,0.68895,0.48495,0.48494,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10029,ERR4648689,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L002_R1_001.fastq.gz 15K1_S4_L002_R2_001.fastq.gz,fastq fastq,1671563912.0,10997131.0,E MTAB 9615:15K1 S4 L002 R,0:76 1:76,A:463642862;C:369576882;G:375034721;T:463043696;N:265751,76,76,,,463642862,369576882,375034721,463043696,265751,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94621,0.95036,0.1321,0.12108,0.68408,0.68838,0.49122,0.47456,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10030,ERR4648690,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L003_R1_001.fastq.gz 15K1_S4_L003_R2_001.fastq.gz,fastq fastq,1750906392.0,11519121.0,E MTAB 9615:15K1 S4 L003 R,0:76 1:76,A:486163392;C:386732615;G:392751931;T:485086491;N:171963,76,76,,,486163392,386732615,392751931,485086491,171963,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94645,0.95048,0.1337,0.12075,0.68515,0.68895,0.48772,0.48793,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10031,ERR4648691,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L004_R1_001.fastq.gz 15K1_S4_L004_R2_001.fastq.gz,fastq fastq,1706814232.0,11229041.0,E MTAB 9615:15K1 S4 L004 R,0:76 1:76,A:473795394;C:377133120;G:382846006;T:472903226;N:136486,76,76,,,473795394,377133120,382846006,472903226,136486,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94725,0.94973,0.13327,0.12016,0.68562,0.68954,0.49105,0.49467,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10032,ERR4648684,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L001_R1_001.fastq.gz 13S6_S9_L001_R2_001.fastq.gz,fastq fastq,1841379680.0,12114340.0,E MTAB 9615:13S6 S9 L001 R,0:76 1:76,A:497786486;C:421002484;G:426037843;T:496245838;N:307029,76,76,,,497786486,421002484,426037843,496245838,307029,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94902,0.95197,0.13858,0.13068,0.67578,0.67821,0.49162,0.5001,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10033,ERR4648685,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L002_R1_001.fastq.gz 13S6_S9_L002_R2_001.fastq.gz,fastq fastq,1800489248.0,11845324.0,E MTAB 9615:13S6 S9 L002 R,0:76 1:76,A:487141754;C:411696441;G:416253811;T:485107559;N:289683,76,76,,,487141754,411696441,416253811,485107559,289683,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94877,0.95202,0.13877,0.13209,0.67219,0.67554,0.49283,0.4882,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10034,ERR4648686,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L003_R1_001.fastq.gz 13S6_S9_L003_R2_001.fastq.gz,fastq fastq,1865349776.0,12272038.0,E MTAB 9615:13S6 S9 L003 R,0:76 1:76,A:504623109;C:426658328;G:431280260;T:502598105;N:189974,76,76,,,504623109,426658328,431280260,502598105,189974,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9488,0.95158,0.1382,0.1322,0.67326,0.67823,0.48581,0.49211,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10035,ERR4648687,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L004_R1_001.fastq.gz 13S6_S9_L004_R2_001.fastq.gz,fastq fastq,1829433392.0,12035746.0,E MTAB 9615:13S6 S9 L004 R,0:76 1:76,A:495172080;C:418346805;G:422823193;T:492947631;N:143683,76,76,,,495172080,418346805,422823193,492947631,143683,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94838,0.95203,0.13783,0.13154,0.67347,0.67702,0.49097,0.48982,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10036,ERR4648680,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L001_R1_001.fastq.gz 13S5_S5_L001_R2_001.fastq.gz,fastq fastq,1764129328.0,11606114.0,E MTAB 9615:13S5 S5 L001 R,0:76 1:76,A:481605171;C:399386009;G:402681794;T:480152811;N:303543,76,76,,,481605171,399386009,402681794,480152811,303543,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94669,0.95053,0.12759,0.12265,0.6758,0.67787,0.48204,0.48571,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10037,ERR4648681,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L002_R1_001.fastq.gz 13S5_S5_L002_R2_001.fastq.gz,fastq fastq,1720255136.0,11317468.0,E MTAB 9615:13S5 S5 L002 R,0:76 1:76,A:469777402;C:389359060;G:392798842;T:468039297;N:280535,76,76,,,469777402,389359060,392798842,468039297,280535,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94584,0.94469,0.12714,0.1201,0.67556,0.67787,0.46946,0.48243,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10038,ERR4648682,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L003_R1_001.fastq.gz 13S5_S5_L003_R2_001.fastq.gz,fastq fastq,1782008784.0,11723742.0,E MTAB 9615:13S5 S5 L003 R,0:76 1:76,A:486839858;C:403504903;G:406596413;T:484891715;N:175895,76,76,,,486839858,403504903,406596413,484891715,175895,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94547,0.94921,0.1273,0.12142,0.67487,0.67724,0.48324,0.48226,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10039,ERR4648683,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L004_R1_001.fastq.gz 13S5_S5_L004_R2_001.fastq.gz,fastq fastq,1745683368.0,11484759.0,E MTAB 9615:13S5 S5 L004 R,0:76 1:76,A:476931443;C:395203177;G:398442382;T:474964685;N:141681,76,76,,,476931443,395203177,398442382,474964685,141681,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94627,0.94906,0.12677,0.12035,0.67551,0.67763,0.47924,0.4843,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10040,ERR4648676,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L001_R1_001.fastq.gz 13S1_S1_L001_R2_001.fastq.gz,fastq fastq,1675492352.0,11022976.0,E MTAB 9615:13S1 S1 L001 R,0:76 1:76,A:455402707;C:380201647;G:385200827;T:454410247;N:276924,76,76,,,455402707,380201647,385200827,454410247,276924,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94815,0.94794,0.12103,0.1129,0.69327,0.69652,0.48471,0.48643,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10041,ERR4648677,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L002_R1_001.fastq.gz 13S1_S1_L002_R2_001.fastq.gz,fastq fastq,1633908192.0,10749396.0,E MTAB 9615:13S1 S1 L002 R,0:76 1:76,A:444126523;C:370832524;G:375586115;T:443096444;N:266586,76,76,,,444126523,370832524,375586115,443096444,266586,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94863,0.95255,0.11967,0.11346,0.6927,0.69566,0.48395,0.48478,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10042,ERR4648678,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L003_R1_001.fastq.gz 13S1_S1_L003_R2_001.fastq.gz,fastq fastq,1698133208.0,11171929.0,E MTAB 9615:13S1 S1 L003 R,0:76 1:76,A:461740823;C:385469489;G:390285009;T:460464431;N:173456,76,76,,,461740823,385469489,390285009,460464431,173456,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94875,0.95192,0.11914,0.11105,0.69353,0.69649,0.48055,0.48273,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10043,ERR4648679,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L004_R1_001.fastq.gz 13S1_S1_L004_R2_001.fastq.gz,fastq fastq,1661636792.0,10931821.0,E MTAB 9615:13S1 S1 L004 R,0:76 1:76,A:451786646;C:377303854;G:381943974;T:450471337;N:130981,76,76,,,451786646,377303854,381943974,450471337,130981,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94966,0.95236,0.11837,0.11148,0.69215,0.6955,0.48615,0.48711,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10044,ERR4648672,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L001_R1_001.fastq.gz 13K6_S10_L001_R2_001.fastq.gz,fastq fastq,1697239752.0,11166051.0,E MTAB 9615:13K6 S10 L001 R,0:76 1:76,A:458337242;C:387675189;G:393817637;T:457129778;N:279906,76,76,,,458337242,387675189,393817637,457129778,279906,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94948,0.95219,0.12998,0.12293,0.67618,0.67848,0.50185,0.49952,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10045,ERR4648673,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L002_R1_001.fastq.gz 13K6_S10_L002_R2_001.fastq.gz,fastq fastq,1673328784.0,11008742.0,E MTAB 9615:13K6 S10 L002 R,0:76 1:76,A:451774513;C:382335962;G:388349370;T:450595018;N:273921,76,76,,,451774513,382335962,388349370,450595018,273921,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94837,0.95265,0.12834,0.12248,0.67515,0.67799,0.49985,0.50072,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10046,ERR4648674,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L003_R1_001.fastq.gz 13K6_S10_L003_R2_001.fastq.gz,fastq fastq,1718962376.0,11308963.0,E MTAB 9615:13K6 S10 L003 R,0:76 1:76,A:464326802;C:392820934;G:398719859;T:462921749;N:173032,76,76,,,464326802,392820934,398719859,462921749,173032,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94887,0.94779,0.12909,0.12199,0.67562,0.67777,0.49225,0.49141,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10047,ERR4648675,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L004_R1_001.fastq.gz 13K6_S10_L004_R2_001.fastq.gz,fastq fastq,1700026824.0,11184387.0,E MTAB 9615:13K6 S10 L004 R,0:76 1:76,A:459161966;C:388439150;G:394446506;T:457846371;N:132831,76,76,,,459161966,388439150,394446506,457846371,132831,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9473,0.95161,0.12897,0.12179,0.67551,0.67811,0.48685,0.4972,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10048,ERR4648668,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L001_R1_001.fastq.gz 13K5_S6_L001_R2_001.fastq.gz,fastq fastq,1790254024.0,11777987.0,E MTAB 9615:13K5 S6 L001 R,0:76 1:76,A:487293594;C:405551734;G:411238332;T:485873462;N:296902,76,76,,,487293594,405551734,411238332,485873462,296902,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94726,0.94704,0.12004,0.11278,0.67533,0.67779,0.48364,0.48388,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10049,ERR4648669,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L002_R1_001.fastq.gz 13K5_S6_L002_R2_001.fastq.gz,fastq fastq,1749029952.0,11506776.0,E MTAB 9615:13K5 S6 L002 R,0:76 1:76,A:476215821;C:396276458;G:401611483;T:474647042;N:279148,76,76,,,476215821,396276458,401611483,474647042,279148,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94762,0.95173,0.12006,0.11284,0.67631,0.68018,0.48241,0.47833,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10050,ERR4648670,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L003_R1_001.fastq.gz 13K5_S6_L003_R2_001.fastq.gz,fastq fastq,1811820544.0,11919872.0,E MTAB 9615:13K5 S6 L003 R,0:76 1:76,A:493339499;C:410551445;G:416118309;T:491625876;N:185415,76,76,,,493339499,410551445,416118309,491625876,185415,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9476,0.94796,0.12002,0.11151,0.67872,0.6802,0.47743,0.47744,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10051,ERR4648671,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L004_R1_001.fastq.gz 13K5_S6_L004_R2_001.fastq.gz,fastq fastq,1774793800.0,11676275.0,E MTAB 9615:13K5 S6 L004 R,0:76 1:76,A:483347019;C:402198669;G:407461838;T:481643127;N:143147,76,76,,,483347019,402198669,407461838,481643127,143147,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9475,0.95165,0.11907,0.11154,0.67734,0.67931,0.46812,0.48622,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10052,ERR4648664,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L001_R1_001.fastq.gz 13K1_S2_L001_R2_001.fastq.gz,fastq fastq,1668503392.0,10976996.0,E MTAB 9615:13K1 S2 L001 R,0:76 1:76,A:454536456;C:377057732;G:382495387;T:454135749;N:278068,76,76,,,454536456,377057732,382495387,454135749,278068,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95225,0.95532,0.12378,0.11159,0.70212,0.70317,0.49492,0.50085,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10053,ERR4648665,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L002_R1_001.fastq.gz 13K1_S2_L002_R2_001.fastq.gz,fastq fastq,1633824136.0,10748843.0,E MTAB 9615:13K1 S2 L002 R,0:76 1:76,A:444960536;C:369666363;G:374403909;T:444522641;N:270687,76,76,,,444960536,369666363,374403909,444522641,270687,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95199,0.95599,0.12228,0.11149,0.70151,0.70437,0.49885,0.49797,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10054,ERR4648666,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L003_R1_001.fastq.gz 13K1_S2_L003_R2_001.fastq.gz,fastq fastq,1692052752.0,11131926.0,E MTAB 9615:13K1 S2 L003 R,0:76 1:76,A:461375866;C:382427180;G:387578702;T:460499241;N:171763,76,76,,,461375866,382427180,387578702,460499241,171763,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95194,0.95208,0.1245,0.11189,0.701,0.70457,0.49831,0.49526,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10055,ERR4648667,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13]  / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water  euthanasia and dissociation through seringe needle Trizol extraction  isopropanol precipitation and RNAeasy column Qiagen  KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13]  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L004_R1_001.fastq.gz 13K1_S2_L004_R2_001.fastq.gz,fastq fastq,1662467776.0,10937288.0,E MTAB 9615:13K1 S2 L004 R,0:76 1:76,A:453180833;C:375869158;G:380805111;T:452478416;N:134258,76,76,,,453180833,375869158,380805111,452478416,134258,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95157,0.95197,0.12307,0.11055,0.7027,0.70544,0.49989,0.49505,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10383,ERR8517249,ERX8083723,ERS10517669,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier control,hnRNPK 003,SAMEA12918519,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003,webin reads hnRNPK 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: hnRNPK 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz,fastq fastq,2931486932.0,19421721.0,webin reads hnRNPK 003,0:75.51 1:75.43,A:759548162;C:700272829;G:700149526;T:770783019;N:733396,75,75,,,759548162,700272829,700149526,770783019,733396,ERX8083723,ERS10517669,ERA8937191,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.9621,0.96378,0.06994,0.06876,0.68757,0.68998,0.46746,0.47041,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10384,ERR8517226,ERX8083700,ERS10517665,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier control,hnRNPK 001,SAMEA12918515,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001,webin reads hnRNPK 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: hnRNPK 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz,fastq fastq,2728299749.0,18074835.0,webin reads hnRNPK 001,0:75.51 1:75.43,A:710869412;C:649804308;G:644363972;T:722599378;N:662679,75,75,,,710869412,649804308,644363972,722599378,662679,ERX8083700,ERS10517665,ERA8936710,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96092,0.96336,0.07296,0.07144,0.68862,0.69209,0.47036,0.47104,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10385,ERR8517194,ERX8083668,ERS10517668,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,RNA control,GFP 003,SAMEA12918518,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: GFP 003,webin reads GFP 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: GFP 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz,fastq fastq,2845571506.0,18850866.0,webin reads GFP 003,0:75.52 1:75.43,A:737412560;C:678774596;G:684567775;T:744108157;N:708418,75,75,,,737412560,678774596,684567775,744108157,708418,ERX8083668,ERS10517668,ERA8936242,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96279,0.96355,0.06774,0.06607,0.68864,0.69183,0.469,0.46906,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10386,ERR8517159,ERX8083633,ERS10517664,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,RNA control,GFP 001,SAMEA12918514,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: GFP 001,webin reads GFP 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: GFP 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz,fastq fastq,2873485447.0,19035162.0,webin reads GFP 001,0:75.52 1:75.44,A:746120172;C:687054955;G:682142981;T:757435799;N:731540,75,75,,,746120172,687054955,682142981,757435799,731540,ERX8083633,ERS10517664,ERA8935703,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96176,0.96461,0.07014,0.06932,0.68672,0.68913,0.47006,0.46794,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10387,ERR8517115,ERX8083589,ERS10517671,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier rescue,91S hnRNPK 003,SAMEA12918521,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003,webin reads 91S hnRNPK 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S hnRNPK 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz,fastq fastq,2853403405.0,18902398.0,webin reads 91S hnRNPK 003,0:75.52 1:75.44,A:739541111;C:681340573;G:681790014;T:750013318;N:718389,75,75,,,739541111,681340573,681790014,750013318,718389,ERX8083589,ERS10517671,ERA8935191,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96234,0.96429,0.0679,0.06627,0.68984,0.69126,0.46434,0.47087,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10388,ERR8517082,ERX8083556,ERS10517667,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier rescue,91S hnRNPK 001,SAMEA12918517,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001,webin reads 91S hnRNPK 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S hnRNPK 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz,fastq fastq,2795603091.0,18519699.0,webin reads 91S hnRNPK 001,0:75.52 1:75.43,A:722724564;C:672552332;G:664566386;T:735058575;N:701234,75,75,,,722724564,672552332,664566386,735058575,701234,ERX8083556,ERS10517667,ERA8934579,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96307,0.96547,0.06551,0.06458,0.68714,0.68856,0.46817,0.46555,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10389,ERR8517039,ERX8083513,ERS10517670,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Toxic condition,91S GFP 003,SAMEA12918520,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003,webin reads 91S GFP 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S GFP 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz,fastq fastq,2946600193.0,19521826.0,webin reads 91S GFP 003,0:75.51 1:75.43,A:763284580;C:704439363;G:702989767;T:775149110;N:737373,75,75,,,763284580,704439363,702989767,775149110,737373,ERX8083513,ERS10517670,ERA8933888,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96151,0.96295,0.06621,0.06481,0.68807,0.69092,0.46928,0.46982,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10390,ERR8516998,ERX8083472,ERS10517666,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Toxic condition,91S GFP 001,SAMEA12918516,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001,webin reads 91S GFP 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S GFP 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz,fastq fastq,2821113913.0,18686946.0,webin reads 91S GFP 001,0:75.52 1:75.44,A:726676187;C:676899384;G:676400816;T:740427303;N:710223,75,75,,,726676187,676899384,676400816,740427303,710223,ERX8083472,ERS10517666,ERA8933211,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96147,0.96465,0.07106,0.06991,0.68822,0.69556,0.47261,0.47451,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
11833,ERR11872224,ERX11269666,ERS16284435,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 9,SAMEA114295326,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295326|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 9|scientific name:Danio rerio|strain:AB|tank:T13,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 9 s,Sample 9 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1100sR1436.fastq.gz,fastq,1961832438.0,38853673.0,E MTAB 13269:Sample 9,0:50.49,A:498124499;C:481739620;G:459005215;T:520487633;N:2475471,50,,,,498124499,481739620,459005215,520487633,2475471,ERX11269666,ERS16284435,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11834,ERR11872220,ERX11269662,ERS16284431,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 5,SAMEA114295322,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295322|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 5|scientific name:Danio rerio|strain:AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 5 s,Sample 5 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1137sR1431.fastq.gz,fastq,1384318515.0,27436121.0,E MTAB 13269:Sample 5,0:50.46,A:351376207;C:340294254;G:322773331;T:366105473;N:3769250,50,,,,351376207,340294254,322773331,366105473,3769250,ERX11269662,ERS16284431,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11835,ERR11872216,ERX11269658,ERS16284427,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 1,SAMEA114295318,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295318|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 1|scientific name:Danio rerio|strain:AB|tank:T7,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 1 s,Sample 1 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1067sR1425.fastq.gz,fastq,2542543911.0,50536210.0,E MTAB 13269:Sample 1,0:50.31,A:650946248;C:611164311;G:577961102;T:679442750;N:23029500,50,,,,650946248,611164311,577961102,679442750,23029500,ERX11269658,ERS16284427,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11836,ERR11872218,ERX11269660,ERS16284429,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 3,SAMEA114295320,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295320|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 3|scientific name:Danio rerio|strain:AB|tank:T7,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 3 s,Sample 3 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1100sR1428.fastq.gz,fastq,1504139674.0,29976579.0,E MTAB 13269:Sample 3,0:50.18,A:378815411;C:361930389;G:348289715;T:391168927;N:23935232,50,,,,378815411,361930389,348289715,391168927,23935232,ERX11269660,ERS16284429,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11837,ERR11872219,ERX11269661,ERS16284430,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 4,SAMEA114295321,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295321|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 4|scientific name:Danio rerio|strain:AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 4 s,Sample 4 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1067sR1429.fastq.gz,fastq,1287164622.0,25539878.0,E MTAB 13269:Sample 4,0:50.40,A:326779989;C:313960441;G:299210114;T:340187543;N:7026535,50,,,,326779989,313960441,299210114,340187543,7026535,ERX11269661,ERS16284430,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11838,ERR11872222,ERX11269664,ERS16284433,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 7,SAMEA114295324,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295324|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 7|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 7|scientific name:Danio rerio|strain:AB|tank:T13,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 7 s,Sample 7 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1067sR1433.fastq.gz,fastq,2055723538.0,40748974.0,E MTAB 13269:Sample 7,0:50.45,A:530988871;C:494680653;G:471905883;T:551730327;N:6417804,50,,,,530988871,494680653,471905883,551730327,6417804,ERX11269664,ERS16284433,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11839,ERR11872221,ERX11269663,ERS16284432,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 6,SAMEA114295323,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295323|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 6|scientific name:Danio rerio|strain:AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 6 s,Sample 6 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1100sR1432.fastq.gz,fastq,1541862753.0,30534298.0,E MTAB 13269:Sample 6,0:50.50,A:390914024;C:378834682;G:362325696;T:407660220;N:2128131,50,,,,390914024,378834682,362325696,407660220,2128131,ERX11269663,ERS16284432,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11840,ERR11872217,ERX11269659,ERS16284428,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 2,SAMEA114295319,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:27Z|ENA LAST UPDATE:2024 01 01T01:03:27Z|External Id:SAMEA114295319|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:27Z|INSDC last update:2024 01 01T01:03:27Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 2|scientific name:Danio rerio|strain:AB|tank:T7,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 2 s,Sample 2 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1067sR1427.fastq.gz,fastq,1120463267.0,22442762.0,E MTAB 13269:Sample 2,0:49.93,A:283544047;C:261601041;G:250663913;T:294648349;N:30005917,49,,,,283544047,261601041,250663913,294648349,30005917,ERX11269659,ERS16284428,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11841,ERR11872223,ERX11269665,ERS16284434,ERP150458,PRJEB65329,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E-MTAB-13269,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole  a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,Sample 8,SAMEA114295325,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295325|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13269:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13269:Sample 8|scientific name:Danio rerio|strain:AB|tank:T13,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,E MTAB 13269:Sample 8 s,Sample 8 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of difenoconazole high exposure and low exposure concentrations in addition to untreated control groups. simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150458,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1067sR1435.fastq.gz,fastq,2492217928.0,49578248.0,E MTAB 13269:Sample 8,0:50.27,A:633127675;C:599191649;G:572355526;T:659345988;N:28197090,50,,,,633127675,599191649,572355526,659345988,28197090,ERX11269665,ERS16284434,ERA26965226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11842,ERR11872230,ERX11269672,ERS16284439,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 4,SAMEA114295330,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295330|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 4|scientific name:Danio rerio|strain:AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 4 s,Sample 4 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s2-R1718-dre-nc-metalaxyl_Eilebrecht.fastq.gz,fastq,3090739917.0,61141982.0,E MTAB 13270:Sample 4,0:50.55,A:757773770;C:707158595;G:708507725;T:915894260;N:1405567,50,,,,757773770,707158595,708507725,915894260,1405567,ERX11269672,ERS16284439,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11843,ERR11872228,ERX11269670,ERS16284437,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 2,SAMEA114295328,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295328|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 2|scientific name:Danio rerio|strain:AB|tank:T6,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 2 s,Sample 2 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s1-R1716-dre-C2-metalaxyl_Eilebrecht.fastq.gz,fastq,2700642168.0,53433052.0,E MTAB 13270:Sample 2,0:50.54,A:669595678;C:619368901;G:590427891;T:819827582;N:1422116,50,,,,669595678,619368901,590427891,819827582,1422116,ERX11269670,ERS16284437,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11844,ERR11872227,ERX11269669,ERS16284436,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 1,SAMEA114295327,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295327|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 1|scientific name:Danio rerio|strain:AB|tank:T6,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 1 s,Sample 1 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s1-R1714-dre-nc-metalaxyl_Eilebrecht.fastq.gz,fastq,2274694218.0,45004376.0,E MTAB 13270:Sample 1,0:50.54,A:562285999;C:518447937;G:499619290;T:693250049;N:1090943,50,,,,562285999,518447937,499619290,693250049,1090943,ERX11269669,ERS16284436,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11845,ERR11872231,ERX11269673,ERS16284440,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 5,SAMEA114295331,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295331|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 5|scientific name:Danio rerio|strain:AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 5 s,Sample 5 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s2-R1720-dre-C2-metalaxyl_Eilebrecht.fastq.gz,fastq,2777053633.0,54933357.0,E MTAB 13270:Sample 5,0:50.55,A:677084481;C:642868295;G:614554344;T:841210183;N:1336330,50,,,,677084481,642868295,614554344,841210183,1336330,ERX11269673,ERS16284440,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11846,ERR11872229,ERX11269671,ERS16284438,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 3,SAMEA114295329,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295329|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 3|scientific name:Danio rerio|strain:AB|tank:T6,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 3 s,Sample 3 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s1-R1717-dre-C3-metalaxyl_Eilebrecht.fastq.gz,fastq,2503234144.0,49524111.0,E MTAB 13270:Sample 3,0:50.55,A:612103203;C:572993175;G:554869755;T:761847743;N:1420268,50,,,,612103203,572993175,554869755,761847743,1420268,ERX11269671,ERS16284438,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11847,ERR11872233,ERX11269675,ERS16284442,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 7,SAMEA114295333,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295333|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 7|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 7|scientific name:Danio rerio|strain:AB|tank:T9,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 7 s,Sample 7 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s3-R1722-dre-nc-metalaxyl_Eilebrecht.fastq.gz,fastq,2210069991.0,43725261.0,E MTAB 13270:Sample 7,0:50.54,A:543075905;C:511224703;G:487348154;T:667396647;N:1024582,50,,,,543075905,511224703,487348154,667396647,1024582,ERX11269675,ERS16284442,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11848,ERR11872234,ERX11269676,ERS16284443,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 8,SAMEA114295334,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295334|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 8|scientific name:Danio rerio|strain:AB|tank:T9,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 8 s,Sample 8 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s3-R1724-dre-C2-metalaxyl_Eilebrecht.fastq.gz,fastq,2289618271.0,45294560.0,E MTAB 13270:Sample 8,0:50.55,A:560540697;C:527453035;G:507883622;T:692636061;N:1104856,50,,,,560540697,527453035,507883622,692636061,1104856,ERX11269676,ERS16284443,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11849,ERR11872235,ERX11269677,ERS16284444,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 9,SAMEA114295335,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295335|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 9|scientific name:Danio rerio|strain:AB|tank:T9,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 9 s,Sample 9 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s3-R1725-dre-C3-metalaxyl_Eilebrecht.fastq.gz,fastq,2164282095.0,42813111.0,E MTAB 13270:Sample 9,0:50.55,A:526798074;C:499625113;G:480175291;T:656576036;N:1107581,50,,,,526798074,499625113,480175291,656576036,1107581,ERX11269677,ERS16284444,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
11850,ERR11872232,ERX11269674,ERS16284441,ERP150460,PRJEB65331,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E-MTAB-13270,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl  a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit.  The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,,Protocols: : at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,Sample 6,SAMEA114295332,Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME),ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295332|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 6|scientific name:Danio rerio|strain:AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,E MTAB 13270:Sample 6 s,Sample 6 s,mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to metalaxyl for xxx hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina  San Diego  USA.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP150460,Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups,ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01,p1201s2-R1721-dre-C3-metalaxyl_Eilebrecht.fastq.gz,fastq,2333796132.0,46171402.0,E MTAB 13270:Sample 6,0:50.55,A:571724946;C:541769310;G:513423860;T:705671180;N:1206836,50,,,,571724946,541769310,513423860,705671180,1206836,ERX11269674,ERS16284441,ERA26965713,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2024-01-01,Undetermined,Embryo,Whole Organism,All anatomical structures
15557,ERR12916374,ERX12288721,ERS18989008,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 4,SAMEA115497325,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 4|scientific name:Danio rerio|strain:Wild type AB|tank:T12,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 4 p,Sample 4 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32227_R2068_dre_nc_fulvestrant_lib661348_10164_3_1.fastq.gz NG-32227_R2068_dre_nc_fulvestrant_lib661348_10164_3_2.fastq.gz,fastq fastq,12187177686.0,40354893.0,E MTAB 14020:NG 32227 R2068 dre nc fulvestrant lib661348 10164 3 ,0:151 1:151,A:3305078518;C:2786935079;G:2833891750;T:3261092784;N:179555,151,151,,,3305078518,2786935079,2833891750,3261092784,179555,ERX12288721,ERS18989008,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15558,ERR12916378,ERX12288725,ERS18989012,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 8,SAMEA115497329,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 8|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 8 p,Sample 8 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32227_R2075_dre_C2_fulvestrant_lib661353_10164_3_1.fastq.gz NG-32227_R2075_dre_C2_fulvestrant_lib661353_10164_3_2.fastq.gz,fastq fastq,11901620680.0,39409340.0,E MTAB 14020:NG 32227 R2075 dre C2 fulvestrant lib661353 10164 3 ,0:151 1:151,A:3237613547;C:2714994048;G:2755289588;T:3193549887;N:173610,151,151,,,3237613547,2714994048,2755289588,3193549887,173610,ERX12288725,ERS18989012,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15559,ERR12916373,ERX12288720,ERS18989007,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 3,SAMEA115497324,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 3|scientific name:Danio rerio|strain:Wild type AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 3 p,Sample 3 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32542_R2066_dre_C3_fulvestrant_lib672119_10184_2_1.fastq.gz NG-32542_R2066_dre_C3_fulvestrant_lib672119_10184_2_2.fastq.gz,fastq fastq,10934088784.0,36205592.0,E MTAB 14020:NG 32542 R2066 dre C3 fulvestrant lib672119 10184 2 ,0:151 1:151,A:2998030197;C:2488169576;G:2491574541;T:2956054160;N:260310,151,151,,,2998030197,2488169576,2491574541,2956054160,260310,ERX12288720,ERS18989007,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15560,ERR12916376,ERX12288723,ERS18989010,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 6,SAMEA115497327,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 6|scientific name:Danio rerio|strain:Wild type AB|tank:T12,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 6 p,Sample 6 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32542_R2071_dre_C3_fulvestrant_lib672120_10184_1_1.fastq.gz NG-32542_R2071_dre_C3_fulvestrant_lib672120_10184_1_2.fastq.gz,fastq fastq,10332415392.0,34213296.0,E MTAB 14020:NG 32542 R2071 dre C3 fulvestrant lib672120 10184 1 ,0:151 1:151,A:2830892520;C:2350292883;G:2358159763;T:2792844342;N:225884,151,151,,,2830892520,2350292883,2358159763,2792844342,225884,ERX12288723,ERS18989010,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15561,ERR12916375,ERX12288722,ERS18989009,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 5,SAMEA115497326,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 5|scientific name:Danio rerio|strain:Wild type AB|tank:T12,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 5 p,Sample 5 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32227_R2070_dre_C2_fulvestrant_lib661350_10164_3_1.fastq.gz NG-32227_R2070_dre_C2_fulvestrant_lib661350_10164_3_2.fastq.gz,fastq fastq,11003883400.0,36436700.0,E MTAB 14020:NG 32227 R2070 dre C2 fulvestrant lib661350 10164 3 ,0:151 1:151,A:2994383363;C:2510974240;G:2552484598;T:2945879588;N:161611,151,151,,,2994383363,2510974240,2552484598,2945879588,161611,ERX12288722,ERS18989009,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15562,ERR12916372,ERX12288719,ERS18989006,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 2,SAMEA115497323,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 2|scientific name:Danio rerio|strain:Wild type AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 2 p,Sample 2 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32227_R2065_dre_C2_fulvestrant_lib661347_10164_3_1.fastq.gz NG-32227_R2065_dre_C2_fulvestrant_lib661347_10164_3_2.fastq.gz,fastq fastq,11419243026.0,37812063.0,E MTAB 14020:NG 32227 R2065 dre C2 fulvestrant lib661347 10164 3 ,0:151 1:151,A:3111236492;C:2602474235;G:2639014496;T:3066349898;N:167905,151,151,,,3111236492,2602474235,2639014496,3066349898,167905,ERX12288719,ERS18989006,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15563,ERR12916379,ERX12288726,ERS18989013,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 9,SAMEA115497330,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 9|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 9 p,Sample 9 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32542_R2076_dre_C3_fulvestrant_lib676805_10195_1_1.fastq.gz NG-32542_R2076_dre_C3_fulvestrant_lib676805_10195_1_2.fastq.gz,fastq fastq,13933360108.0,46136954.0,E MTAB 14020:NG 32542 R2076 dre C3 fulvestrant lib676805 10195 1 ,0:151 1:151,A:3755178070;C:3212497786;G:3265644027;T:3699709369;N:330856,151,151,,,3755178070,3212497786,3265644027,3699709369,330856,ERX12288726,ERS18989013,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15564,ERR12916371,ERX12288718,ERS18989005,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 1,SAMEA115497322,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 1|scientific name:Danio rerio|strain:Wild type AB|tank:T8,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 1 p,Sample 1 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32227_R2063_dre_nc_fulvestrant_lib661345_10164_3_1.fastq.gz NG-32227_R2063_dre_nc_fulvestrant_lib661345_10164_3_2.fastq.gz,fastq fastq,9751334172.0,32289186.0,E MTAB 14020:NG 32227 R2063 dre nc fulvestrant lib661345 10164 3 ,0:151 1:151,A:2644860460;C:2230247028;G:2268943823;T:2607137645;N:145216,151,151,,,2644860460,2230247028,2268943823,2607137645,145216,ERX12288718,ERS18989005,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15565,ERR12916377,ERX12288724,ERS18989011,ERP159620,PRJEB75017,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E-MTAB-14020,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 7,SAMEA115497328,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14020:Sample 7|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14020:Sample 7|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,E MTAB 14020:Sample 7 p,Sample 7 p,mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.    RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159620,Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32227_R2073_dre_nc_fulvestrant_lib661351_10164_3_1.fastq.gz NG-32227_R2073_dre_nc_fulvestrant_lib661351_10164_3_2.fastq.gz,fastq fastq,11826951482.0,39162091.0,E MTAB 14020:NG 32227 R2073 dre nc fulvestrant lib661351 10164 3 ,0:151 1:151,A:3220473968;C:2696879564;G:2734502253;T:3174923177;N:172520,151,151,,,3220473968,2696879564,2734502253,3174923177,172520,ERX12288724,ERS18989011,ERA29606970,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15566,ERR12916383,ERX12288730,ERS18989113,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 4,SAMEA115497430,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 4|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 4 p,Sample 4 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2128_dre_nc_estradiol_lib672208_10184_2_1.fastq.gz NG-32544_R2128_dre_nc_estradiol_lib672208_10184_2_2.fastq.gz,fastq fastq,11519262406.0,38143253.0,E MTAB 14022:NG 32544 R2128 dre nc estradiol lib672208 10184 2 ,0:151 1:151,A:3155893663;C:2615447205;G:2624126192;T:3123521216;N:274130,151,151,,,3155893663,2615447205,2624126192,3123521216,274130,ERX12288730,ERS18989113,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15567,ERR12916382,ERX12288729,ERS18989112,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 3,SAMEA115497429,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 3|scientific name:Danio rerio|strain:Wild type AB|tank:T8,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 3 p,Sample 3 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2126_dre_C3_estradiol_lib672207_10184_2_1.fastq.gz NG-32544_R2126_dre_C3_estradiol_lib672207_10184_2_2.fastq.gz,fastq fastq,9989685860.0,33078430.0,E MTAB 14022:NG 32544 R2126 dre C3 estradiol lib672207 10184 2 ,0:151 1:151,A:2726397137;C:2282307054;G:2282386674;T:2698356730;N:238265,151,151,,,2726397137,2282307054,2282386674,2698356730,238265,ERX12288729,ERS18989112,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15568,ERR12916384,ERX12288731,ERS18989114,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 5,SAMEA115497431,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 5|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 5 p,Sample 5 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2130_dre_C2_estradiol_lib672209_10184_2_1.fastq.gz NG-32544_R2130_dre_C2_estradiol_lib672209_10184_2_2.fastq.gz,fastq fastq,12577165386.0,41646243.0,E MTAB 14022:NG 32544 R2130 dre C2 estradiol lib672209 10184 2 ,0:151 1:151,A:3461907353;C:2843697550;G:2849814020;T:3421444968;N:301495,151,151,,,3461907353,2843697550,2849814020,3421444968,301495,ERX12288731,ERS18989114,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15569,ERR12916380,ERX12288727,ERS18989110,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 1,SAMEA115497427,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 1|scientific name:Danio rerio|strain:Wild type AB|tank:T8,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 1 p,Sample 1 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2123_dre_nc_estradiol_lib676807_10195_2_1.fastq.gz NG-32544_R2123_dre_nc_estradiol_lib676807_10195_2_2.fastq.gz,fastq fastq,9678660288.0,32048544.0,E MTAB 14022:NG 32544 R2123 dre nc estradiol lib676807 10195 2 ,0:151 1:151,A:2651923654;C:2190605826;G:2231831230;T:2604055145;N:244433,151,151,,,2651923654,2190605826,2231831230,2604055145,244433,ERX12288727,ERS18989110,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15570,ERR12916381,ERX12288728,ERS18989111,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 2,SAMEA115497428,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 2|scientific name:Danio rerio|strain:Wild type AB|tank:T8,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 2 p,Sample 2 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2125_dre_C2_estradiol_lib672206_10184_2_1.fastq.gz NG-32544_R2125_dre_C2_estradiol_lib672206_10184_2_2.fastq.gz,fastq fastq,11431327556.0,37852078.0,E MTAB 14022:NG 32544 R2125 dre C2 estradiol lib672206 10184 2 ,0:151 1:151,A:3138124320;C:2596000456;G:2590788209;T:3106140537;N:274034,151,151,,,3138124320,2596000456,2590788209,3106140537,274034,ERX12288728,ERS18989111,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15571,ERR12916386,ERX12288733,ERS18989116,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 7,SAMEA115497433,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 7|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 7|scientific name:Danio rerio|strain:Wild type AB|tank:T19,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 7 p,Sample 7 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2133_dre_nc_estradiol_lib672211_10184_1_1.fastq.gz NG-32544_R2133_dre_nc_estradiol_lib672211_10184_1_2.fastq.gz,fastq fastq,13575436654.0,44951777.0,E MTAB 14022:NG 32544 R2133 dre nc estradiol lib672211 10184 1 ,0:151 1:151,A:3755208011;C:3052011499;G:3055003729;T:3712919528;N:293887,151,151,,,3755208011,3052011499,3055003729,3712919528,293887,ERX12288733,ERS18989116,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15572,ERR12916385,ERX12288732,ERS18989115,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 6,SAMEA115497432,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 6|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 6 p,Sample 6 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2131_dre_C3_estradiol_lib672210_10184_1_1.fastq.gz NG-32544_R2131_dre_C3_estradiol_lib672210_10184_1_2.fastq.gz,fastq fastq,13579439362.0,44965031.0,E MTAB 14022:NG 32544 R2131 dre C3 estradiol lib672210 10184 1 ,0:151 1:151,A:3748627643;C:3057631445;G:3066968241;T:3705917099;N:294934,151,151,,,3748627643,3057631445,3066968241,3705917099,294934,ERX12288732,ERS18989115,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15573,ERR12916388,ERX12288735,ERS18989118,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 9,SAMEA115497435,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 9|scientific name:Danio rerio|strain:Wild type AB|tank:T19,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 9 p,Sample 9 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2136_dre_C3_estradiol_lib672213_10184_1_1.fastq.gz NG-32544_R2136_dre_C3_estradiol_lib672213_10184_1_2.fastq.gz,fastq fastq,11908180120.0,39431060.0,E MTAB 14022:NG 32544 R2136 dre C3 estradiol lib672213 10184 1 ,0:151 1:151,A:3272028142;C:2696935524;G:2712854157;T:3226102684;N:259613,151,151,,,3272028142,2696935524,2712854157,3226102684,259613,ERX12288735,ERS18989118,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15574,ERR12916387,ERX12288734,ERS18989117,ERP159621,PRJEB75018,mRNA  Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups,E-MTAB-14022,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 8,SAMEA115497434,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14022:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 8|scientific name:Danio rerio|strain:Wild type AB|tank:T19,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,E MTAB 14022:Sample 8 p,Sample 8 p,mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159621,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-32544_R2135_dre_C2_estradiol_lib672212_10184_2_1.fastq.gz NG-32544_R2135_dre_C2_estradiol_lib672212_10184_2_2.fastq.gz,fastq fastq,15738562088.0,52114444.0,E MTAB 14022:NG 32544 R2135 dre C2 estradiol lib672212 10184 2 ,0:151 1:151,A:4308214612;C:3581781339;G:3588099342;T:4260093303;N:373492,151,151,,,4308214612,3581781339,3588099342,4260093303,373492,ERX12288734,ERS18989117,ERA29607067,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15575,ERR12916390,ERX12288737,ERS18989120,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 2,SAMEA115497437,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 2|scientific name:Danio rerio|strain:Wild type AB|tank:T5,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 2 p,Sample 2 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2197_dre_C2_bisphenola_lib692361_10227_1_1.fastq.gz NG-33234_R2197_dre_C2_bisphenola_lib692361_10227_1_2.fastq.gz,fastq fastq,16285232824.0,53924612.0,E MTAB 14023:NG 33234 R2197 dre C2 bisphenola lib692361 10227 1 ,0:151 1:151,A:4518199560;C:3645980414;G:3674232653;T:4446656777;N:163420,151,151,,,4518199560,3645980414,3674232653,4446656777,163420,ERX12288737,ERS18989120,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15576,ERR12916393,ERX12288740,ERS18989123,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 5,SAMEA115497440,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 5|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 5|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 5 p,Sample 5 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2202_dre_C2_bisphenola_lib692364_10224_3_1.fastq.gz NG-33234_R2202_dre_C2_bisphenola_lib692364_10224_3_2.fastq.gz,fastq fastq,14761516588.0,48879194.0,E MTAB 14023:NG 33234 R2202 dre C2 bisphenola lib692364 10224 3 ,0:151 1:151,A:4115762614;C:3282831633;G:3308598262;T:4054111375;N:212704,151,151,,,4115762614,3282831633,3308598262,4054111375,212704,ERX12288740,ERS18989123,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15577,ERR12916396,ERX12288743,ERS18989126,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 8,SAMEA115497443,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 8|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 8|scientific name:Danio rerio|strain:Wild type AB|tank:T19,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 8 p,Sample 8 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2207_dre_C2_bisphenola_lib692367_10227_1_1.fastq.gz NG-33234_R2207_dre_C2_bisphenola_lib692367_10227_1_2.fastq.gz,fastq fastq,13161143692.0,43579946.0,E MTAB 14023:NG 33234 R2207 dre C2 bisphenola lib692367 10227 1 ,0:151 1:151,A:3624299194;C:2976559804;G:2995115250;T:3565037596;N:131848,151,151,,,3624299194,2976559804,2995115250,3565037596,131848,ERX12288743,ERS18989126,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15578,ERR12916392,ERX12288739,ERS18989122,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 4,SAMEA115497439,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 4|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 4|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 4 p,Sample 4 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2200_dre_nc_bisphenola_lib692363_10227_2_1.fastq.gz NG-33234_R2200_dre_nc_bisphenola_lib692363_10227_2_2.fastq.gz,fastq fastq,26147833460.0,86582230.0,E MTAB 14023:NG 33234 R2200 dre nc bisphenola lib692363 10227 2 ,0:151 1:151,A:7258232055;C:5842879066;G:5902714067;T:7142264329;N:1743943,151,151,,,7258232055,5842879066,5902714067,7142264329,1743943,ERX12288739,ERS18989122,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15579,ERR12916394,ERX12288741,ERS18989124,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 6,SAMEA115497441,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 6|scientific name:Danio rerio|strain:Wild type AB|tank:T18,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 6 p,Sample 6 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2203_dre_C3_bisphenola_lib692365_10224_3_1.fastq.gz NG-33234_R2203_dre_C3_bisphenola_lib692365_10224_3_2.fastq.gz,fastq fastq,21922257010.0,72590255.0,E MTAB 14023:NG 33234 R2203 dre C3 bisphenola lib692365 10224 3 ,0:151 1:151,A:6045629984;C:4936064183;G:4974917873;T:5965326250;N:318720,151,151,,,6045629984,4936064183,4974917873,5965326250,318720,ERX12288741,ERS18989124,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15580,ERR12916397,ERX12288744,ERS18989127,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 9,SAMEA115497444,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 9|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 9|scientific name:Danio rerio|strain:Wild type AB|tank:T19,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 9 p,Sample 9 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2208_dre_C3_bisphenola_lib692368_10227_2_1.fastq.gz NG-33234_R2208_dre_C3_bisphenola_lib692368_10227_2_2.fastq.gz,fastq fastq,23881298998.0,79077149.0,E MTAB 14023:NG 33234 R2208 dre C3 bisphenola lib692368 10227 2 ,0:151 1:151,A:6507764646;C:5454501673;G:5496344023;T:6421103639;N:1585017,151,151,,,6507764646,5454501673,5496344023,6421103639,1585017,ERX12288744,ERS18989127,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15581,ERR12916391,ERX12288738,ERS18989121,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 3,SAMEA115497438,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 3|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 3|scientific name:Danio rerio|strain:Wild type AB|tank:T5,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 3 p,Sample 3 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2198_dre_C3_bisphenola_lib692362_10227_2_1.fastq.gz NG-33234_R2198_dre_C3_bisphenola_lib692362_10227_2_2.fastq.gz,fastq fastq,24214884272.0,80181736.0,E MTAB 14023:NG 33234 R2198 dre C3 bisphenola lib692362 10227 2 ,0:151 1:151,A:6702079295;C:5424413438;G:5474562552;T:6612208700;N:1620287,151,151,,,6702079295,5424413438,5474562552,6612208700,1620287,ERX12288738,ERS18989121,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures
15582,ERR12916389,ERX12288736,ERS18989119,ERP159622,PRJEB75019,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E-MTAB-14023,Transcriptome Analysis,In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A  according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours  simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally  potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,,Protocols: at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,Sample 1,SAMEA115497436,"Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)",ENA first public:2024 11 26|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for molecular biology and applied ecology IME|INSDC status:public|Submitter Id:E MTAB 14023:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14023:Sample 1|scientific name:Danio rerio|strain:Wild type AB|tank:T5,,,,,,,,,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,E MTAB 14023:Sample 1 p,Sample 1 p,mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,at the end of exposure  10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals  Irvine  USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel  Düren  Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent  Santa Clara  USA. Samples were stored at  80°C.   RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription  cDNA libraries was produced from mRNA fragments and ligated to the adapters.,,ssRNA-seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP159622,Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups,ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26,NG-33234_R2195_dre_nc_bisphenola_lib692360_10227_2_1.fastq.gz NG-33234_R2195_dre_nc_bisphenola_lib692360_10227_2_2.fastq.gz,fastq fastq,23247776686.0,76979393.0,E MTAB 14023:NG 33234 R2195 dre nc bisphenola lib692360 10227 2 ,0:151 1:151,A:6402000447;C:5235790040;G:5291162202;T:6317305100;N:1518897,151,151,,,6402000447,5235790040,5291162202,6317305100,1518897,ERX12288736,ERS18989119,ERA29607068,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2024-11-26,Undetermined,Embryo,Whole Organism,All anatomical structures