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
79,DRR032745,DRX029551,DRS049950,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 50 individuals,Dr 60h 2,SAMD00028142,,sample name:Dr 60h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028142,DRX029551,Dr 60h 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028142,,,,3875337000.0,38753370.0,DRR032745,0:100 1:0,A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983,100,0,,,1042558903,899892111,896867583,1035981420,36983,DRX029551,DRS049950,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.91891,,0.09445,,0.66156,,0.45564,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Hatching,Embryo,Whole Organism,All anatomical structures
80,DRR032744,DRX029550,DRS049949,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 50 individuals,Dr 60h 1,SAMD00028141,,sample name:Dr 60h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028141,DRX029550,Dr 60h 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028141,,,,3538468200.0,35384682.0,DRR032744,0:100 1:0,A:960664313;C:812459988;G:809014008;T:956295205;N:34686,100,0,,,960664313,812459988,809014008,956295205,34686,DRX029550,DRS049949,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.91388,,0.10346,,0.66076,,0.45203,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Hatching,Embryo,Whole Organism,All anatomical structures
84,DRR032740,DRX029546,DRS049945,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 50 individuals,Dr 48h 2,SAMD00028137,,sample name:Dr 48h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028137,DRX029546,Dr 48h 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028137,,,,3702804700.0,37028047.0,DRR032740,0:100 1:0,A:993931475;C:862403562;G:857808891;T:988623734;N:37038,100,0,,,993931475,862403562,857808891,988623734,37038,DRX029546,DRS049945,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92508,,0.08526,,0.68349,,0.45769,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Hatching,Embryo,Whole Organism,All anatomical structures
85,DRR032739,DRX029545,DRS049944,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 50 individuals,Dr 48h 1,SAMD00028136,,sample name:Dr 48h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028136,DRX029545,Dr 48h 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028136,,,,3980240400.0,39802404.0,DRR032739,0:100 1:0,A:1070497788;C:925240883;G:920038728;T:1064422474;N:40527,100,0,,,1070497788,925240883,920038728,1064422474,40527,DRX029545,DRS049944,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.92349,,0.08681,,0.67874,,0.46565,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Hatching,Embryo,Whole Organism,All anatomical structures
9764,ERR3454281,ERX3476201,ERS360451,ERP116513,PRJEB33700,Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila,ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961,Other,Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional  translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However  the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,,SAMEA2224102,SC,ArrayExpress DevelopmentalStage:Hatching   long pec   pec fin   ZFS:0000033   ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224102|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 4. A 5 base indexing sequence CAAGA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|scientific name:Danio rerio|strain:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP116513,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,659815100.0,13196302.0,ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 6,0:50,A:163494131;C:142490716;G:153472608;T:200319869;N:37776,50,,,,163494131,142490716,153472608,200319869,37776,ERX3476201,ERS360451,ERA2051096,CIRI-Inserm-U1111|European Nucleotide Archive,CIRI-Inserm-U1111,1,0.00278,,0.00206,,0.99922,,0.24031,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2014-03-04,Hatching,Embryo,Whole Organism,All anatomical structures
9765,ERR3454280,ERX3476200,ERS360450,ERP116513,PRJEB33700,Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila,ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961,Other,Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional  translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However  the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,,SAMEA2224101,SC,ArrayExpress DevelopmentalStage:Hatching   long pec   pec fin   ZFS:0000033   ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224101|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype32 clutch 4. A 5 base indexing sequence CGCAA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|scientific name:Danio rerio|strain:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP116513,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,1031629900.0,20632598.0,ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 5,0:50,A:266496533;C:234318648;G:214719546;T:316013013;N:82160,50,,,,266496533,234318648,214719546,316013013,82160,ERX3476200,ERS360450,ERA2051096,CIRI-Inserm-U1111|European Nucleotide Archive,CIRI-Inserm-U1111,1,0.003,,0.00187,,0.99902,,0.27272,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2014-03-04,Hatching,Embryo,Whole Organism,All anatomical structures
9766,ERR3454279,ERX3476199,ERS360449,ERP116513,PRJEB33700,Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila,ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961,Other,Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional  translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However  the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,,SAMEA2224100,SC,ArrayExpress DevelopmentalStage:Hatching   long pec   pec fin   ZFS:0000033   ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224100|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence GCACG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|scientific name:Danio rerio|strain:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP116513,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,547730200.0,10954604.0,ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 4,0:50,A:142048050;C:118592881;G:112867934;T:174179317;N:42018,50,,,,142048050,118592881,112867934,174179317,42018,ERX3476199,ERS360449,ERA2051096,CIRI-Inserm-U1111|European Nucleotide Archive,CIRI-Inserm-U1111,1,0.00355,,0.00226,,0.99902,,0.30487,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2014-03-04,Hatching,Embryo,Whole Organism,All anatomical structures
9767,ERR3454278,ERX3476198,ERS360448,ERP116513,PRJEB33700,Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila,ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961,Other,Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional  translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However  the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,,SAMEA2224099,SC,ArrayExpress DevelopmentalStage:Hatching   long pec   pec fin   ZFS:0000033   ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224099|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence CAGAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|scientific name:Danio rerio|strain:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP116513,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,844323050.0,16886461.0,ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 3,0:50,A:219263127;C:181661743;G:173433057;T:269898556;N:66567,50,,,,219263127,181661743,173433057,269898556,66567,ERX3476198,ERS360448,ERA2051096,CIRI-Inserm-U1111|European Nucleotide Archive,CIRI-Inserm-U1111,1,0.00523,,0.00319,,0.99892,,0.2637,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2014-03-04,Hatching,Embryo,Whole Organism,All anatomical structures
9768,ERR3454277,ERX3476197,ERS360447,ERP116513,PRJEB33700,Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila,ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961,Other,Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional  translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However  the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,,SAMEA2224098,SC,ArrayExpress DevelopmentalStage:Hatching   long pec   pec fin   ZFS:0000033   ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224098|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence AGAAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|scientific name:Danio rerio|strain:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP116513,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,600000000.0,12000000.0,ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 2,0:50,A:153130383;C:136248892;G:127363796;T:183213089;N:43840,50,,,,153130383,136248892,127363796,183213089,43840,ERX3476197,ERS360447,ERA2051096,CIRI-Inserm-U1111|European Nucleotide Archive,CIRI-Inserm-U1111,1,0.00372,,0.00211,,0.99888,,0.31649,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2014-03-04,Hatching,Embryo,Whole Organism,All anatomical structures
9769,ERR3454276,ERX3476196,ERS360446,ERP116513,PRJEB33700,Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila,ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961,Other,Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional  translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However  the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,,SAMEA2224097,SC,ArrayExpress DevelopmentalStage:Hatching   long pec   pec fin   ZFS:0000033   ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224097|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence GAGGC is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|scientific name:Danio rerio|strain:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP116513,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26,,,600000000.0,12000000.0,ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 1,0:50,A:153852410;C:135392627;G:125428239;T:185280608;N:46116,50,,,,153852410,135392627,125428239,185280608,46116,ERX3476196,ERS360446,ERA2051096,CIRI-Inserm-U1111|European Nucleotide Archive,CIRI-Inserm-U1111,1,0.00545,,0.00291,,0.9988,,0.31681,,50,,T,,under 1.2% mapping rate,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2014-03-04,Hatching,Embryo,Whole Organism,All anatomical structures
10309,ERR7179904,ERX6749461,ERS8138767,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1287,SAMEA10486022,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486022|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1287|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1287|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1287 s,R1287 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1287_sr.fastq.gz,fastq,2134815688.0,42280846.0,E MTAB 11092:R1287,0:50.49,A:565052096;C:502336362;G:482125031;T:582647501;N:2654698,50,,,,565052096,502336362,482125031,582647501,2654698,ERX6749461,ERS8138767,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.9356,,0.11997,,0.68314,,0.47934,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10310,ERR7179903,ERX6749460,ERS8138766,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1284,SAMEA10486020,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486020|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1284|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1284|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1284 s,R1284 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1284_sr.fastq.gz,fastq,2050986060.0,40612707.0,E MTAB 11092:R1284,0:50.50,A:538161680;C:490403596;G:466089424;T:554663872;N:1667488,50,,,,538161680,490403596,466089424,554663872,1667488,ERX6749460,ERS8138766,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93753,,0.1231,,0.68479,,0.45919,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10311,ERR7179902,ERX6749459,ERS8138765,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1275,SAMEA10486018,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486018|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1275|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1275|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1275 s,R1275 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1275_sr.fastq.gz,fastq,1157613512.0,22947522.0,E MTAB 11092:R1275,0:50.45,A:299754053;C:277899399;G:266613838;T:309994905;N:3351317,50,,,,299754053,277899399,266613838,309994905,3351317,ERX6749459,ERS8138765,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.9411,,0.10048,,0.69008,,0.47233,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10312,ERR7179901,ERX6749458,ERS8138764,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1272,SAMEA10486016,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486016|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1272|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1272|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1272 s,R1272 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1272_sr.fastq.gz,fastq,1634309317.0,32374943.0,E MTAB 11092:R1272,0:50.48,A:424752350;C:392450289;G:375596049;T:438931453;N:2579176,50,,,,424752350,392450289,375596049,438931453,2579176,ERX6749458,ERS8138764,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93744,,0.10119,,0.68627,,0.47078,,47,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10313,ERR7179900,ERX6749457,ERS8138763,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1269,SAMEA10486014,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486014|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1269|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1269|sex:mixed|stimulus:control|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1269 s,R1269 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1269_sr.fastq.gz,fastq,1209767720.0,23959130.0,E MTAB 11092:R1269,0:50.49,A:311532826;C:293995213;G:280433261;T:322310486;N:1495934,50,,,,311532826,293995213,280433261,322310486,1495934,ERX6749457,ERS8138763,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94226,,0.10041,,0.68777,,0.45677,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10314,ERR7179899,ERX6749456,ERS8138762,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1289,SAMEA10486012,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486012|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1289|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1289|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1289 s,R1289 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1289_sr.fastq.gz,fastq,2336898428.0,46306897.0,E MTAB 11092:R1289,0:50.47,A:612494442;C:551754242;G:532830428;T:633879257;N:5940059,50,,,,612494442,551754242,532830428,633879257,5940059,ERX6749456,ERS8138762,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93744,,0.13096,,0.68753,,0.49027,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10315,ERR7179898,ERX6749455,ERS8138761,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1286,SAMEA10486010,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486010|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1286|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1286|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1286 s,R1286 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1286_sr.fastq.gz,fastq,2816827872.0,55797255.0,E MTAB 11092:R1286,0:50.48,A:736348159;C:671023504;G:643914486;T:761242852;N:4298871,50,,,,736348159,671023504,643914486,761242852,4298871,ERX6749455,ERS8138761,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94033,,0.11711,,0.68477,,0.46969,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10316,ERR7179897,ERX6749454,ERS8138760,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1277,SAMEA10486008,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486008|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1277|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1277|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1277 s,R1277 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,p946sR1277_sr.fastq.gz,fastq,1268705881.0,25118834.0,E MTAB 11092:R1277,0:50.51 1:0,A:329102604;C:306045954;G:293488785;T:339279603;N:788935,50,0,,,329102604,306045954,293488785,339279603,788935,ERX6749454,ERS8138760,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94045,,0.11288,,0.69025,,0.47095,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10317,ERR7179896,ERX6749453,ERS8138759,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1274,SAMEA10486006,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486006|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1274|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1274|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1274 s,R1274 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1274_sr.fastq.gz,fastq,1107133784.0,21923109.0,E MTAB 11092:R1274,0:50.50,A:289596768;C:264193186;G:253295296;T:299245790;N:802744,50,,,,289596768,264193186,253295296,299245790,802744,ERX6749453,ERS8138759,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93893,,0.1111,,0.68091,,0.46331,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10318,ERR7179895,ERX6749452,ERS8138758,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1271,SAMEA10486004,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486004|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1271|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1271|sex:mixed|stimulus:control|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1271 s,R1271 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1271_sr.fastq.gz,fastq,1998122568.0,39583977.0,E MTAB 11092:R1271,0:50.48,A:518205942;C:480545742;G:459346718;T:536870486;N:3153680,50,,,,518205942,480545742,459346718,536870486,3153680,ERX6749452,ERS8138758,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94252,,0.10542,,0.67886,,0.47083,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10319,ERR7179894,ERX6749451,ERS8138757,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1288,SAMEA10486002,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486002|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1288|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1288|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1288 s,R1288 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1288_sr.fastq.gz,fastq,1892621026.0,37517169.0,E MTAB 11092:R1288,0:50.45,A:498344488;C:444226431;G:428956415;T:514938257;N:6155435,50,,,,498344488,444226431,428956415,514938257,6155435,ERX6749451,ERS8138757,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93409,,0.12599,,0.68692,,0.47741,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10320,ERR7179893,ERX6749450,ERS8138756,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1285,SAMEA10486000,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486000|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1285|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1285|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1285 s,R1285 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1285_sr.fastq.gz,fastq,1829128750.0,36225046.0,E MTAB 11092:R1285,0:50.49,A:478165041;C:438683413;G:419515205;T:490751870;N:2013221,50,,,,478165041,438683413,419515205,490751870,2013221,ERX6749450,ERS8138756,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93814,,0.11901,,0.68639,,0.46045,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10321,ERR7179892,ERX6749449,ERS8138755,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1276,SAMEA10485998,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10485998|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1276|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1276|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1276 s,R1276 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1276_sr.fastq.gz,fastq,1575013709.0,31202630.0,E MTAB 11092:R1276,0:50.48,A:406866583;C:380336879;G:364368178;T:420970851;N:2471218,50,,,,406866583,380336879,364368178,420970851,2471218,ERX6749449,ERS8138755,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.9399,,0.10316,,0.68564,,0.45479,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10322,ERR7179891,ERX6749448,ERS8138754,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1273,SAMEA10485996,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10485996|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1273|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1273|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1273 s,R1273 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1273_sr.fastq.gz,fastq,978769211.0,19384726.0,E MTAB 11092:R1273,0:50.49,A:254759436;C:235060632;G:224944252;T:262789193;N:1215698,50,,,,254759436,235060632,224944252,262789193,1215698,ERX6749448,ERS8138754,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93731,,0.114,,0.68812,,0.46237,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10323,ERR7179890,ERX6749447,ERS8138753,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4  0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity  Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 µL of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R1270,SAMEA10485994,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10485994|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1270|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1270|sex:mixed|stimulus:control|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1270 s,R1270 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1270_sr.fastq.gz,fastq,1079683414.0,21379121.0,E MTAB 11092:R1270,0:50.50,A:282457582;C:258094012;G:247325987;T:291030099;N:775734,50,,,,282457582,258094012,247325987,291030099,775734,ERX6749447,ERS8138753,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93758,,0.10619,,0.68363,,0.47429,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10452,ERR9267591,ERX8810014,ERS10996143,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393652,University of Heidelberg,Compound:2 Mhex|Concentration:110.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393652|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run4 C09|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC10 48h run4 C09|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC10 48h run4 C09 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC10_48h_run4_C09.fastq.gz,fastq,73547800.0,1470956.0,S TOXR1835:S 2 Mhex EC10 48h run4 C09 r,0:50,A:15203281;C:19662939;G:18154185;T:20526838;N:557,50,,,,15203281,19662939,18154185,20526838,557,ERX8810014,ERS10996143,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10458,ERR9267534,ERX8809957,ERS10996086,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393595,University of Heidelberg,Compound:VPA|Concentration:43.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393595|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC10 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC10 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC10 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC10_48h_run2.fastq.gz,fastq,67366250.0,1347325.0,S TOXR1835:S VPA EC10 48h run2 r,0:50,A:13717398;C:17804386;G:16137194;T:19706738;N:534,50,,,,13717398,17804386,16137194,19706738,534,ERX8809957,ERS10996086,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10461,ERR9267561,ERX8809984,ERS10996113,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393622,University of Heidelberg,Compound:2 Ebut|Concentration:340.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393622|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC20 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC20 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC20 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC20_48h_run3.fastq.gz,fastq,78064750.0,1561295.0,S TOXR1835:S 2 Ebut EC20 48h run3 r,0:50,A:15756649;C:20956143;G:18904818;T:22446503;N:637,50,,,,15756649,20956143,18904818,22446503,637,ERX8809984,ERS10996113,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10466,ERR9267593,ERX8810016,ERS10996145,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393654,University of Heidelberg,Compound:H2O|Concentration:nan nan|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393654|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S NK 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S NK 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S NK 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_NK_48h_run5.fastq.gz,fastq,71625600.0,1432512.0,S TOXR1835:S NK 48h run5 r,0:50,A:14725047;C:18910123;G:17229035;T:20760764;N:631,50,,,,14725047,18910123,17229035,20760764,631,ERX8810016,ERS10996145,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10468,ERR9267590,ERX8810013,ERS10996142,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393651,University of Heidelberg,Compound:2 Mhex|Concentration:221.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393651|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run4 B09|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC10 48h run4 B09|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC10 48h run4 B09 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC10_48h_run4_B09.fastq.gz,fastq,78479400.0,1569588.0,S TOXR1835:S 2 Mhex EC10 48h run4 B09 r,0:50,A:16162085;C:20836101;G:18922307;T:22558262;N:645,50,,,,16162085,20836101,18922307,22558262,645,ERX8810013,ERS10996142,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10470,ERR9267573,ERX8809996,ERS10996125,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393634,University of Heidelberg,Compound:DMSO|Concentration:0.1 %|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393634|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S DMSO 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S DMSO 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S DMSO 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_DMSO_48h_run4.fastq.gz,fastq,73082100.0,1461642.0,S TOXR1835:S DMSO 48h run4 r,0:50,A:14881867;C:19585099;G:17922397;T:20692144;N:593,50,,,,14881867,19585099,17922397,20692144,593,ERX8809996,ERS10996125,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10476,ERR9267535,ERX8809958,ERS10996087,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393596,University of Heidelberg,Compound:VPA|Concentration:21.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393596|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA 1 2EC10 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA 1 2EC10 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA 1 2EC10 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_1-2EC10_48h_run2.fastq.gz,fastq,73399450.0,1467989.0,S TOXR1835:S VPA 1 2EC10 48h run2 r,0:50,A:14822778;C:19573143;G:17695184;T:21307767;N:578,50,,,,14822778,19573143,17695184,21307767,578,ERX8809958,ERS10996087,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10479,ERR9267523,ERX8809946,ERS10996075,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393584,University of Heidelberg,Compound:2 Mhex|Concentration:253.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393584|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC20 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC20 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC20 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC20_48h_run1.fastq.gz,fastq,68542050.0,1370841.0,S TOXR1835:S 2 Mhex EC20 48h run1 r,0:50,A:14024232;C:18238849;G:16815901;T:19462492;N:576,50,,,,14024232,18238849,16815901,19462492,576,ERX8809946,ERS10996075,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10480,ERR9267578,ERX8810001,ERS10996130,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393639,University of Heidelberg,Compound:VPA|Concentration:43.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393639|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC10 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC10 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC10 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC10_48h_run4.fastq.gz,fastq,74138000.0,1482760.0,S TOXR1835:S VPA EC10 48h run4 r,0:50,A:15200941;C:19770845;G:18010004;T:21155539;N:671,50,,,,15200941,19770845,18010004,21155539,671,ERX8810001,ERS10996130,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10484,ERR9267579,ERX8810002,ERS10996131,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393640,University of Heidelberg,Compound:VPA|Concentration:21.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393640|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA 1 2EC10 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA 1 2EC10 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA 1 2EC10 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_1-2EC10_48h_run4.fastq.gz,fastq,71560000.0,1431200.0,S TOXR1835:S VPA 1 2EC10 48h run4 r,0:50,A:14689062;C:19057908;G:17423224;T:20389200;N:606,50,,,,14689062,19057908,17423224,20389200,606,ERX8810002,ERS10996131,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10486,ERR9267524,ERX8809947,ERS10996076,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393585,University of Heidelberg,Compound:2 Mhex|Concentration:221.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393585|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC10 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC10 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC10_48h_run1.fastq.gz,fastq,66823650.0,1336473.0,S TOXR1835:S 2 Mhex EC10 48h run1 r,0:50,A:13627080;C:17870281;G:16395274;T:18930502;N:513,50,,,,13627080,17870281,16395274,18930502,513,ERX8809947,ERS10996076,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10487,ERR9267569,ERX8809992,ERS10996121,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393630,University of Heidelberg,Compound:2 Mhex|Concentration:110.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393630|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex 1 2EC10 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex 1 2EC10 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex 1 2EC10 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_1-2EC10_48h_run3.fastq.gz,fastq,68861900.0,1377238.0,S TOXR1835:S 2 Mhex 1 2EC10 48h run3 r,0:50,A:13973560;C:18399768;G:16700087;T:19787899;N:586,50,,,,13973560,18399768,16700087,19787899,586,ERX8809992,ERS10996121,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10489,ERR9267513,ERX8809936,ERS10996065,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393574,University of Heidelberg,Compound:VPA|Concentration:21.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393574|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA 1 2EC10 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA 1 2EC10 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA 1 2EC10 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_1-2EC10_48h_run1.fastq.gz,fastq,63721950.0,1274439.0,S TOXR1835:S VPA 1 2EC10 48h run1 r,0:50,A:13080828;C:17351354;G:15603067;T:17686116;N:585,50,,,,13080828,17351354,15603067,17686116,585,ERX8809936,ERS10996065,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10494,ERR9267525,ERX8809948,ERS10996077,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393586,University of Heidelberg,Compound:2 Mhex|Concentration:110.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393586|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex 1 2EC10 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex 1 2EC10 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex 1 2EC10 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_1-2EC10_48h_run1.fastq.gz,fastq,67408050.0,1348161.0,S TOXR1835:S 2 Mhex 1 2EC10 48h run1 r,0:50,A:13792359;C:17904560;G:16483974;T:19226594;N:563,50,,,,13792359,17904560,16483974,19226594,563,ERX8809948,ERS10996077,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10496,ERR9267511,ERX8809934,ERS10996063,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393572,University of Heidelberg,Compound:VPA|Concentration:54.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393572|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC20 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC20 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC20 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC20_48h_run1.fastq.gz,fastq,70277250.0,1405545.0,S TOXR1835:S VPA EC20 48h run1 r,0:50,A:14198964;C:19021887;G:17302994;T:19752851;N:554,50,,,,14198964,19021887,17302994,19752851,554,ERX8809934,ERS10996063,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10497,ERR9267556,ERX8809979,ERS10996108,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393617,University of Heidelberg,Compound:VPA|Concentration:43.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393617|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC10 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC10 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC10 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC10_48h_run3.fastq.gz,fastq,69142000.0,1382840.0,S TOXR1835:S VPA EC10 48h run3 r,0:50,A:13995831;C:18385053;G:16704246;T:20056299;N:571,50,,,,13995831,18385053,16704246,20056299,571,ERX8809979,ERS10996108,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10500,ERR9267551,ERX8809974,ERS10996103,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393612,University of Heidelberg,Compound:DMSO|Concentration:0.1 %|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393612|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S DMSO 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S DMSO 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S DMSO 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_DMSO_48h_run3.fastq.gz,fastq,60861450.0,1217229.0,S TOXR1835:S DMSO 48h run3 r,0:50,A:12333828;C:16098263;G:14632351;T:17796489;N:519,50,,,,12333828,16098263,14632351,17796489,519,ERX8809974,ERS10996103,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10501,ERR9267568,ERX8809991,ERS10996120,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393629,University of Heidelberg,Compound:2 Mhex|Concentration:221.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393629|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC10 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC10 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC10_48h_run3.fastq.gz,fastq,68035550.0,1360711.0,S TOXR1835:S 2 Mhex EC10 48h run3 r,0:50,A:13826663;C:18115373;G:16605120;T:19487836;N:558,50,,,,13826663,18115373,16605120,19487836,558,ERX8809991,ERS10996120,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10502,ERR9267585,ERX8810008,ERS10996137,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393646,University of Heidelberg,Compound:2 Ebut|Concentration:139.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393646|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut 1 2EC10 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut 1 2EC10 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut 1 2EC10 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_1-2EC10_48h_run4.fastq.gz,fastq,74677950.0,1493559.0,S TOXR1835:S 2 Ebut 1 2EC10 48h run4 r,0:50,A:15203705;C:19865728;G:18407584;T:21200325;N:608,50,,,,15203705,19865728,18407584,21200325,608,ERX8810008,ERS10996137,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10513,ERR9267539,ERX8809962,ERS10996091,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393600,University of Heidelberg,Compound:2 Ebut|Concentration:340.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393600|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC20 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC20 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC20 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC20_48h_run2.fastq.gz,fastq,67424650.0,1348493.0,S TOXR1835:S 2 Ebut EC20 48h run2 r,0:50,A:13694254;C:18014496;G:16206609;T:19508741;N:550,50,,,,13694254,18014496,16206609,19508741,550,ERX8809962,ERS10996091,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10517,ERR9267584,ERX8810007,ERS10996136,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393645,University of Heidelberg,Compound:2 Ebut|Concentration:278.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393645|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC10 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC10 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC10 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC10_48h_run4.fastq.gz,fastq,70090700.0,1401814.0,S TOXR1835:S 2 Ebut EC10 48h run4 r,0:50,A:14240762;C:18647482;G:17073445;T:20128406;N:605,50,,,,14240762,18647482,17073445,20128406,605,ERX8810007,ERS10996136,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10521,ERR9267611,ERX8810034,ERS10996163,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393672,University of Heidelberg,Compound:2 Mhex|Concentration:253.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393672|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC20 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC20 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC20 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC20_48h_run5.fastq.gz,fastq,69905350.0,1398107.0,S TOXR1835:S 2 Mhex EC20 48h run5 r,0:50,A:14517997;C:18401099;G:16823939;T:20161750;N:565,50,,,,14517997,18401099,16823939,20161750,565,ERX8810034,ERS10996163,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10525,ERR9267527,ERX8809950,ERS10996079,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393588,University of Heidelberg,Compound:H2O|Concentration:nan nan|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393588|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S NK 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S NK 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S NK 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_NK_48h_run2.fastq.gz,fastq,69118500.0,1382370.0,S TOXR1835:S NK 48h run2 r,0:50,A:14136001;C:18163834;G:16786976;T:20031136;N:553,50,,,,14136001,18163834,16786976,20031136,553,ERX8809950,ERS10996079,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10529,ERR9267518,ERX8809941,ERS10996070,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393579,University of Heidelberg,Compound:2 Ebut|Concentration:278.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393579|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC10 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC10 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC10 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC10_48h_run1.fastq.gz,fastq,75266500.0,1505330.0,S TOXR1835:S 2 Ebut EC10 48h run1 r,0:50,A:15221491;C:20236124;G:18292558;T:21515646;N:681,50,,,,15221491,20236124,18292558,21515646,681,ERX8809941,ERS10996070,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10532,ERR9267507,ERX8809930,ERS10996059,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393568,University of Heidelberg,Compound:DMSO|Concentration:0.1 %|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393568|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S DMSO 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S DMSO 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S DMSO 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_DMSO_48h_run1.fastq.gz,fastq,67554500.0,1351090.0,S TOXR1835:S DMSO 48h run1 r,0:50,A:13499007;C:18082251;G:16703769;T:19268869;N:604,50,,,,13499007,18082251,16703769,19268869,604,ERX8809930,ERS10996059,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10534,ERR9267571,ERX8809994,ERS10996123,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393632,University of Heidelberg,Compound:H2O|Concentration:nan nan|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393632|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S NK 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S NK 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S NK 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_NK_48h_run4.fastq.gz,fastq,72037700.0,1440754.0,S TOXR1835:S NK 48h run4 r,0:50,A:14745794;C:19202607;G:17512611;T:20576149;N:539,50,,,,14745794,19202607,17512611,20576149,539,ERX8809994,ERS10996123,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10539,ERR9267562,ERX8809985,ERS10996114,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393623,University of Heidelberg,Compound:2 Ebut|Concentration:278.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393623|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC10 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC10 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC10 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC10_48h_run3.fastq.gz,fastq,67908650.0,1358173.0,S TOXR1835:S 2 Ebut EC10 48h run3 r,0:50,A:13740262;C:18142439;G:16364747;T:19660619;N:583,50,,,,13740262,18142439,16364747,19660619,583,ERX8809985,ERS10996114,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10542,ERR9267577,ERX8810000,ERS10996129,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393638,University of Heidelberg,Compound:VPA|Concentration:54.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393638|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC20 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC20 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC20 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC20_48h_run4.fastq.gz,fastq,72161650.0,1443233.0,S TOXR1835:S VPA EC20 48h run4 r,0:50,A:14871161;C:19270264;G:17837781;T:20181814;N:630,50,,,,14871161,19270264,17837781,20181814,630,ERX8810000,ERS10996129,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10546,ERR9267549,ERX8809972,ERS10996101,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393610,University of Heidelberg,Compound:H2O|Concentration:nan nan|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393610|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S NK 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S NK 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S NK 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_NK_48h_run3.fastq.gz,fastq,66542850.0,1330857.0,S TOXR1835:S NK 48h run3 r,0:50,A:13510144;C:17455383;G:16160281;T:19416444;N:598,50,,,,13510144,17455383,16160281,19416444,598,ERX8809972,ERS10996101,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10548,ERR9267563,ERX8809986,ERS10996115,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393624,University of Heidelberg,Compound:2 Ebut|Concentration:139.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393624|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut 1 2EC10 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut 1 2EC10 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut 1 2EC10 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_1-2EC10_48h_run3.fastq.gz,fastq,60900900.0,1218018.0,S TOXR1835:S 2 Ebut 1 2EC10 48h run3 r,0:50,A:12410877;C:16198724;G:14618554;T:17672248;N:497,50,,,,12410877,16198724,14618554,17672248,497,ERX8809986,ERS10996115,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10551,ERR9267607,ERX8810030,ERS10996159,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393668,University of Heidelberg,Compound:2 Ebut|Concentration:139.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393668|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut 1 2EC10 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut 1 2EC10 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut 1 2EC10 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_1-2EC10_48h_run5.fastq.gz,fastq,77392800.0,1547856.0,S TOXR1835:S 2 Ebut 1 2EC10 48h run5 r,0:50,A:15730501;C:20403721;G:19014742;T:22243210;N:626,50,,,,15730501,20403721,19014742,22243210,626,ERX8810030,ERS10996159,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10553,ERR9267519,ERX8809942,ERS10996071,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393580,University of Heidelberg,Compound:2 Ebut|Concentration:139.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393580|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut 1 2EC10 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut 1 2EC10 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut 1 2EC10 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_1-2EC10_48h_run1.fastq.gz,fastq,72942450.0,1458849.0,S TOXR1835:S 2 Ebut 1 2EC10 48h run1 r,0:50,A:14793102;C:19587590;G:17790376;T:20770862;N:520,50,,,,14793102,19587590,17790376,20770862,520,ERX8809942,ERS10996071,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10554,ERR9267541,ERX8809964,ERS10996093,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393602,University of Heidelberg,Compound:2 Ebut|Concentration:139.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393602|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut 1 2EC10 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut 1 2EC10 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut 1 2EC10 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_1-2EC10_48h_run2.fastq.gz,fastq,76523500.0,1530470.0,S TOXR1835:S 2 Ebut 1 2EC10 48h run2 r,0:50,A:15471207;C:20517558;G:18610047;T:21924105;N:583,50,,,,15471207,20517558,18610047,21924105,583,ERX8809964,ERS10996093,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10557,ERR9267505,ERX8809928,ERS10996057,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393566,University of Heidelberg,Compound:H2O|Concentration:nan nan|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393566|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S NK 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S NK 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S NK 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_NK_48h_run1.fastq.gz,fastq,70453750.0,1409075.0,S TOXR1835:S NK 48h run1 r,0:50,A:14163774;C:18922311;G:17592711;T:19774383;N:571,50,,,,14163774,18922311,17592711,19774383,571,ERX8809928,ERS10996057,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10560,ERR9267533,ERX8809956,ERS10996085,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393594,University of Heidelberg,Compound:VPA|Concentration:54.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393594|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC20 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC20 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC20 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC20_48h_run2.fastq.gz,fastq,66631450.0,1332629.0,S TOXR1835:S VPA EC20 48h run2 r,0:50,A:13583196;C:17640936;G:15931969;T:19474795;N:554,50,,,,13583196,17640936,15931969,19474795,554,ERX8809956,ERS10996085,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10561,ERR9267546,ERX8809969,ERS10996098,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393607,University of Heidelberg,Compound:2 Mhex|Concentration:221.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393607|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC10 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC10 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC10_48h_run2.fastq.gz,fastq,69391250.0,1387825.0,S TOXR1835:S 2 Mhex EC10 48h run2 r,0:50,A:14061451;C:18482829;G:16834845;T:20011594;N:531,50,,,,14061451,18482829,16834845,20011594,531,ERX8809969,ERS10996098,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10571,ERR9267589,ERX8810012,ERS10996141,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393650,University of Heidelberg,Compound:2 Mhex|Concentration:253.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393650|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC20 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC20 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC20 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC20_48h_run4.fastq.gz,fastq,73471850.0,1469437.0,S TOXR1835:S 2 Mhex EC20 48h run4 r,0:50,A:15182153;C:19485922;G:17921518;T:20881652;N:605,50,,,,15182153,19485922,17921518,20881652,605,ERX8810012,ERS10996141,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10572,ERR9267595,ERX8810018,ERS10996147,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393656,University of Heidelberg,Compound:DMSO|Concentration:0.1 %|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393656|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S DMSO 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S DMSO 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S DMSO 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_DMSO_48h_run5.fastq.gz,fastq,483150.0,9663.0,S TOXR1835:S DMSO 48h run5 r,0:50,A:132538;C:123309;G:102107;T:125195;N:1,50,,,,132538,123309,102107,125195,1,ERX8810018,ERS10996147,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10573,ERR9267545,ERX8809968,ERS10996097,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393606,University of Heidelberg,Compound:2 Mhex|Concentration:253.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393606|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC20 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC20 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC20 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC20_48h_run2.fastq.gz,fastq,69703750.0,1394075.0,S TOXR1835:S 2 Mhex EC20 48h run2 r,0:50,A:14195637;C:18573126;G:16963229;T:19971173;N:585,50,,,,14195637,18573126,16963229,19971173,585,ERX8809968,ERS10996097,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10576,ERR9267605,ERX8810028,ERS10996157,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393666,University of Heidelberg,Compound:2 Ebut|Concentration:340.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393666|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC20 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC20 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC20 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC20_48h_run5.fastq.gz,fastq,67412850.0,1348257.0,S TOXR1835:S 2 Ebut EC20 48h run5 r,0:50,A:13766964;C:17757638;G:16672345;T:19215358;N:545,50,,,,13766964,17757638,16672345,19215358,545,ERX8810028,ERS10996157,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10580,ERR9267612,ERX8810035,ERS10996164,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393673,University of Heidelberg,Compound:2 Mhex|Concentration:221.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393673|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC10 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC10 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC10_48h_run5.fastq.gz,fastq,66876800.0,1337536.0,S TOXR1835:S 2 Mhex EC10 48h run5 r,0:50,A:13834575;C:17625681;G:16026254;T:19389760;N:530,50,,,,13834575,17625681,16026254,19389760,530,ERX8810035,ERS10996164,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10586,ERR9267583,ERX8810006,ERS10996135,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393644,University of Heidelberg,Compound:2 Ebut|Concentration:340.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393644|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC20 48h run4|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC20 48h run4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC20 48h run4 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC20_48h_run4.fastq.gz,fastq,79026950.0,1580539.0,S TOXR1835:S 2 Ebut EC20 48h run4 r,0:50,A:16191989;C:20840113;G:19258881;T:22735319;N:648,50,,,,16191989,20840113,19258881,22735319,648,ERX8810006,ERS10996135,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10587,ERR9267613,ERX8810036,ERS10996165,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,S TOXR1835:S 2 Mhex 1 2EC10 48h run5,,Treatment:repeated dose|Treatment scheme:daily|organism:Danio rerio|cell line:null|Compound:2 Mhex|scientific name:Danio rerio|Concentration:110.5 µM|Exposure time:48 hpf name:zebrafish|ENA LAST UPDATE:2022 03 15,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex 1 2EC10 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_1-2EC10_48h_run5.fastq.gz,fastq,66428550.0,1328571.0,S TOXR1835:S 2 Mhex 1 2EC10 48h run5 r,0:50,A:13662294;C:17664056;G:16182301;T:18919344;N:555,50,,,,13662294,17664056,16182301,18919344,555,ERX8810036,ERS10996165,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10589,ERR9267540,ERX8809963,ERS10996092,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393601,University of Heidelberg,Compound:2 Ebut|Concentration:278.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393601|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC10 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC10 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC10 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC10_48h_run2.fastq.gz,fastq,64438900.0,1288778.0,S TOXR1835:S 2 Ebut EC10 48h run2 r,0:50,A:13013730;C:17191568;G:15496489;T:18736544;N:569,50,,,,13013730,17191568,15496489,18736544,569,ERX8809963,ERS10996092,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10590,ERR9267599,ERX8810022,ERS10996151,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393660,University of Heidelberg,Compound:VPA|Concentration:54.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393660|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC20 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC20 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC20 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC20_48h_run5.fastq.gz,fastq,62577300.0,1251546.0,S TOXR1835:S VPA EC20 48h run5 r,0:50,A:12927528;C:16490152;G:15013269;T:18145828;N:523,50,,,,12927528,16490152,15013269,18145828,523,ERX8810022,ERS10996151,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10595,ERR9267517,ERX8809940,ERS10996069,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393578,University of Heidelberg,Compound:2 Ebut|Concentration:340.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393578|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Ebut EC20 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Ebut EC20 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC20 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC20_48h_run1.fastq.gz,fastq,73931850.0,1478637.0,S TOXR1835:S 2 Ebut EC20 48h run1 r,0:50,A:14923927;C:19913225;G:18289511;T:20804610;N:577,50,,,,14923927,19913225,18289511,20804610,577,ERX8809940,ERS10996069,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10602,ERR9267529,ERX8809952,ERS10996081,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393590,University of Heidelberg,Compound:DMSO|Concentration:0.1 %|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393590|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S DMSO 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S DMSO 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S DMSO 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_DMSO_48h_run2.fastq.gz,fastq,71101200.0,1422024.0,S TOXR1835:S DMSO 48h run2 r,0:50,A:14497088;C:18633880;G:17219984;T:20749637;N:611,50,,,,14497088,18633880,17219984,20749637,611,ERX8809952,ERS10996081,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10604,ERR9267567,ERX8809990,ERS10996119,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393628,University of Heidelberg,Compound:2 Mhex|Concentration:253.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393628|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex EC20 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex EC20 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex EC20 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_EC20_48h_run3.fastq.gz,fastq,68889400.0,1377788.0,S TOXR1835:S 2 Mhex EC20 48h run3 r,0:50,A:14105273;C:18364899;G:16733064;T:19685604;N:560,50,,,,14105273,18364899,16733064,19685604,560,ERX8809990,ERS10996119,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10608,ERR9267555,ERX8809978,ERS10996107,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393616,University of Heidelberg,Compound:VPA|Concentration:54.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393616|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:05Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC20 48h run3|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC20 48h run3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC20 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC20_48h_run3.fastq.gz,fastq,74544700.0,1490894.0,S TOXR1835:S VPA EC20 48h run3 r,0:50,A:15276457;C:19927478;G:18142128;T:21198080;N:557,50,,,,15276457,19927478,18142128,21198080,557,ERX8809978,ERS10996107,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10609,ERR9267606,ERX8810029,ERS10996158,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,S TOXR1835:S 2 Ebut EC10 48h run5,,Treatment:repeated dose|Treatment scheme:daily|organism:Danio rerio|cell line:null|Compound:2 Ebut|scientific name:Danio rerio|Concentration:278.0 µM|Exposure time:48 hpf name:zebrafish|ENA LAST UPDATE:2022 03 15,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Ebut EC10 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Ebut_EC10_48h_run5.fastq.gz,fastq,74809150.0,1496183.0,S TOXR1835:S 2 Ebut EC10 48h run5 r,0:50,A:15289611;C:19739104;G:18188745;T:21591144;N:546,50,,,,15289611,19739104,18188745,21591144,546,ERX8810029,ERS10996158,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10611,ERR9267600,ERX8810023,ERS10996152,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393661,University of Heidelberg,Compound:VPA|Concentration:43.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393661|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:06Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC10 48h run5|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC10 48h run5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC10 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC10_48h_run5.fastq.gz,fastq,66933400.0,1338668.0,S TOXR1835:S VPA EC10 48h run5 r,0:50,A:13563920;C:17744966;G:16018510;T:19605421;N:583,50,,,,13563920,17744966,16018510,19605421,583,ERX8810023,ERS10996152,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10613,ERR9267512,ERX8809935,ERS10996064,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393573,University of Heidelberg,Compound:VPA|Concentration:43.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393573|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:03Z|INSDC status:public|Submitter Id:S TOXR1835:S VPA EC10 48h run1|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S VPA EC10 48h run1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA EC10 48h run1 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_EC10_48h_run1.fastq.gz,fastq,74515500.0,1490310.0,S TOXR1835:S VPA EC10 48h run1 r,0:50,A:14918959;C:20202214;G:18256549;T:21137183;N:595,50,,,,14918959,20202214,18256549,21137183,595,ERX8809935,ERS10996064,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10618,ERR9267557,ERX8809980,ERS10996109,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,S TOXR1835:S VPA 1 2EC10 48h run3,,Treatment:repeated dose|Treatment scheme:daily|organism:Danio rerio|cell line:null|Compound:VPA|scientific name:Danio rerio|Concentration:21.5 µM|Exposure time:48 hpf name:zebrafish|ENA LAST UPDATE:2022 03 15,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA 1 2EC10 48h run3 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_1-2EC10_48h_run3.fastq.gz,fastq,64259050.0,1285181.0,S TOXR1835:S VPA 1 2EC10 48h run3 r,0:50,A:13075721;C:17144963;G:15448716;T:18589136;N:514,50,,,,13075721,17144963,15448716,18589136,514,ERX8809980,ERS10996109,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10620,ERR9267601,ERX8810024,ERS10996153,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,S TOXR1835:S VPA 1 2EC10 48h run5,,Treatment:repeated dose|Treatment scheme:daily|organism:Danio rerio|cell line:null|Compound:VPA|scientific name:Danio rerio|Concentration:21.5 µM|Exposure time:48 hpf name:zebrafish|ENA LAST UPDATE:2022 03 15,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S VPA 1 2EC10 48h run5 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_VPA_1-2EC10_48h_run5.fastq.gz,fastq,72083750.0,1441675.0,S TOXR1835:S VPA 1 2EC10 48h run5 r,0:50,A:14776717;C:19029282;G:17151119;T:21126048;N:584,50,,,,14776717,19029282,17151119,21126048,584,ERX8810024,ERS10996153,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10622,ERR9267547,ERX8809970,ERS10996099,ERP136287,PRJEB51640,CS2 UHEI DART 96 120h raw data EUT080,S-TOXR1835,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13393608,University of Heidelberg,Compound:2 Mhex|Concentration:110.5 µM|ENA first public:2024 03 15|Exposure time:48 hpf Id:SAMEA13393608|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:42:04Z|INSDC status:public|Submitter Id:S TOXR1835:S 2 Mhex 1 2EC10 48h run2|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1835:S 2 Mhex 1 2EC10 48h run2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1835:S 2 Mhex 1 2EC10 48h run2 e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136287,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_2-Mhex_1-2EC10_48h_run2.fastq.gz,fastq,66991750.0,1339835.0,S TOXR1835:S 2 Mhex 1 2EC10 48h run2 r,0:50,A:13672674;C:17839869;G:16313161;T:19165508;N:538,50,,,,13672674,17839869,16313161,19165508,538,ERX8809970,ERS10996099,ERA10091655,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10635,ERR9269920,ERX8812317,ERS10998383,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13395729,University of Heidelberg,Compound:VPA|Concentration:2.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf|External Id:SAMEA13395729|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:53:12Z|INSDC status:public|Submitter Id:S TOXR1832:S 48hpf VPA2 UHEI|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1832:S 48hpf VPA2 UHEI|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf VPA2 UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_VPA2_UHEI.fastq.gz,fastq,47599250.0,951985.0,S TOXR1832:S 48hpf VPA2 UHEI r,0:50,A:9888024;C:12159720;G:11046493;T:14498755;N:6258,50,,,,9888024,12159720,11046493,14498755,6258,ERX8812317,ERS10998383,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10636,ERR9269908,ERX8812305,ERS10998371,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13395717,University of Heidelberg,Compound:VPA|Concentration:200.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf|External Id:SAMEA13395717|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:53:12Z|INSDC status:public|Submitter Id:S TOXR1832:S 48hpf VPA200 UHEI|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1832:S 48hpf VPA200 UHEI|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf VPA200 UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_VPA200_UHEI.fastq.gz,fastq,79585850.0,1591717.0,S TOXR1832:S 48hpf VPA200 UHEI r,0:50,A:16570024;C:20607975;G:18883064;T:23514364;N:10423,50,,,,16570024,20607975,18883064,23514364,10423,ERX8812305,ERS10998371,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10637,ERR9269905,ERX8812302,ERS10998367,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13395714,University of Heidelberg,Compound:DMSO|Concentration:0.1 %|ENA first public:2024 03 15|Exposure time:48 hpf|External Id:SAMEA13395714|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:53:12Z|INSDC status:public|Submitter Id:S TOXR1832:S 48hpf DMSO UHEI|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1832:S 48hpf DMSO UHEI|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf DMSO UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_DMSO_UHEI.fastq.gz,fastq,81583950.0,1631679.0,S TOXR1832:S 48hpf DMSO UHEI r,0:50,A:16850155;C:21271726;G:19396178;T:24055405;N:10486,50,,,,16850155,21271726,19396178,24055405,10486,ERX8812302,ERS10998367,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10640,ERR9269917,ERX8812314,ERS10998380,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13395726,University of Heidelberg,Compound:VPA|Concentration:10.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf|External Id:SAMEA13395726|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:53:12Z|INSDC status:public|Submitter Id:S TOXR1832:S 48hpf VPA10 UHEI|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1832:S 48hpf VPA10 UHEI|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf VPA10 UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_VPA10_UHEI.fastq.gz,fastq,67426000.0,1348520.0,S TOXR1832:S 48hpf VPA10 UHEI r,0:50,A:14029838;C:17712723;G:16312528;T:19361892;N:9019,50,,,,14029838,17712723,16312528,19361892,9019,ERX8812314,ERS10998380,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10642,ERR9269902,ERX8812299,ERS10998364,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13395711,University of Heidelberg,Compound:H2O|Concentration:nan µM|ENA first public:2024 03 15|Exposure time:48 hpf|External Id:SAMEA13395711|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:53:11Z|INSDC status:public|Submitter Id:S TOXR1832:S 48hpf NK UHEI|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1832:S 48hpf NK UHEI|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf NK UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_NK_UHEI.fastq.gz,fastq,62338300.0,1246766.0,S TOXR1832:S 48hpf NK UHEI r,0:50,A:12918525;C:16663516;G:15757264;T:16990654;N:8341,50,,,,12918525,16663516,15757264,16990654,8341,ERX8812299,ERS10998364,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10644,ERR9269914,ERX8812311,ERS10998377,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,S TOXR1832:S 48hpf VPA50 UHEI,,Treatment:repeated dose|Treatment scheme:daily|organism:Danio rerio|cell line:null|Compound:VPA|scientific name:Danio rerio|Concentration:50.0 µM|Exposure time:48 hpf|Gender:null|common name:zebrafish|ENA LAST UPDATE:2022 03 15,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf VPA50 UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_VPA50_UHEI.fastq.gz,fastq,91147100.0,1822942.0,S TOXR1832:S 48hpf VPA50 UHEI r,0:50,A:18945872;C:23376297;G:21393442;T:27419150;N:12339,50,,,,18945872,23376297,21393442,27419150,12339,ERX8812311,ERS10998377,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
10646,ERR9269911,ERX8812308,ERS10998374,ERP136288,PRJEB51641,CS2 UHEI DART 96 120h raw data EUT053,S-TOXR1832,Transcriptome Analysis,,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,,,,SAMEA13395720,University of Heidelberg,Compound:VPA|Concentration:100.0 µM|ENA first public:2024 03 15|Exposure time:48 hpf|External Id:SAMEA13395720|Gender:null|INSDC center name:University of Heidelberg|INSDC last update:2022 03 15T10:53:12Z|INSDC status:public|Submitter Id:S TOXR1832:S 48hpf VPA100 UHEI|Treatment:repeated dose|Treatment scheme:daily|broker name:EU ToxRisk DCC|cell line:null|common name:zebrafish|sample name:S TOXR1832:S 48hpf VPA100 UHEI|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 sequencing,S TOXR1832:S 48hpf VPA100 UHEI e,,TempO Seq library,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP136288,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2024 03 15|ENA LAST UPDATE:2024 03 15,S_48hpf_VPA100_UHEI.fastq.gz,fastq,76050250.0,1521005.0,S TOXR1832:S 48hpf VPA100 UHEI r,0:50,A:15772070;C:19270371;G:17451795;T:23545874;N:10140,50,,,,15772070,19270371,17451795,23545874,10140,ERX8812308,ERS10998374,ERA10091710,EMBL EBI,EMBL EBI,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2022-03-15,Hatching,Embryo,Cell Line,Cell Line
19087,ERR13834862,ERX13237628,ERS21098715,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC1 S20 R1 001.fastq.gz,SAMEA116100635,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 48 HC1,webin reads 48 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 HC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48HC1_S20_R1_001.fastq.gz,fastq,3768442091.0,38065677.0,webin reads 48 HC1,0:99.00,A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200,99,,,,1055463738,792073627,817607736,1103223790,73200,ERX13237628,ERS21098715,ERA30883416,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19088,ERR13834951,ERX13237717,ERS21098721,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR3 S26 R1 001.fastq.gz,58 PR3,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR3,webin reads 58 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR3_S26_R1_001.fastq.gz,fastq,3869469736.0,38850717.0,webin reads 58 PR3,0:99.60,A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717,99,,,,1103909449,804146524,827344036,1134036010,33717,ERX13237717,ERS21098721,ERA30883529,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19089,ERR13835010,ERX13237776,ERS21098726,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC4 S31 R1 001.fastq.gz,SAMEA116100646,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 58 AC4,webin reads 58 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC4_S31_R1_001.fastq.gz,fastq,3607648651.0,36331933.0,webin reads 58 AC4,0:99.30,A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094,99,,,,1038047870,736262498,759315202,1073962987,60094,ERX13237776,ERS21098726,ERA30883721,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19090,ERR13822794,ERX13225546,ERS21098708,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48PR2 S13 R1 001.fastq.gz,48 PR2,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 PR2,webin reads 48 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48PR2_S13_R1_001.fastq.gz,fastq,3809299607.0,38404185.0,webin reads 48 PR2,0:99.19,A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777,99,,,,1067728192,802585802,828435932,1110435904,113777,ERX13225546,ERS21098708,ERA30879682,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19091,ERR13834854,ERX13237620,ERS21098714,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48AC4 S19 R1 001.fastq.gz,48 AC4,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 AC4,webin reads 48 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48AC4_S19_R1_001.fastq.gz,fastq,3410801894.0,34443068.0,webin reads 48 AC4,0:99.03,A:966160063;C:707754156;G:733039262;T:1003772756;N:75657,99,,,,966160063,707754156,733039262,1003772756,75657,ERX13237620,ERS21098714,ERA30883390,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19092,ERR13828824,ERX13231590,ERS21098710,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48PR4 S15 R1 001.fastq.gz,48 PR4,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 PR4,webin reads 48 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 PR4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48PR4_S15_R1_001.fastq.gz,fastq,4365943927.0,44278278.0,webin reads 48 PR4,0:98.60,A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503,98,,,,1214448497,927512154,957491418,1266385355,106503,ERX13231590,ERS21098710,ERA30883309,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19093,ERR13834993,ERX13237759,ERS21098723,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC1 S28 R1 001.fastq.gz,58 AC1,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 AC1,webin reads 58 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC1_S28_R1_001.fastq.gz,fastq,3710768269.0,37364763.0,webin reads 58 AC1,0:99.31,A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465,99,,,,1060419097,761984557,786533722,1101603428,227465,ERX13237759,ERS21098723,ERA30883659,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19094,ERR13834875,ERX13237641,ERS21098717,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC3 S22 R1 001.fastq.gz,48 HC3,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 HC3,webin reads 48 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 HC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48HC3_S22_R1_001.fastq.gz,fastq,3083078586.0,31073491.0,webin reads 48 HC3,0:99.22,A:856250957;C:655140994;G:677078911;T:894558582;N:49142,99,,,,856250957,655140994,677078911,894558582,49142,ERX13237641,ERS21098717,ERA30883447,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19095,ERR13834899,ERX13237665,ERS21098720,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR2 S25 R1 001.fastq.gz,58 PR2,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR2,webin reads 58 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR2_S25_R1_001.fastq.gz,fastq,3849571818.0,38706841.0,webin reads 58 PR2,0:99.45,A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547,99,,,,1089593011,803322469,827777017,1128836774,42547,ERX13237665,ERS21098720,ERA30883518,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19096,ERR13834889,ERX13237655,ERS21098719,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR1 S24 R1 001.fastq.gz,58 PR1,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR1,webin reads 58 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR1_S24_R1_001.fastq.gz,fastq,3945671240.0,39514922.0,webin reads 58 PR1,0:99.85,A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802,99,,,,1135075173,807489123,827964380,1175109762,32802,ERX13237655,ERS21098719,ERA30883497,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19097,ERR13835019,ERX13237785,ERS21098728,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58HC2 S33 R1 001.fastq.gz,SAMEA116100648,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 58 HC2,webin reads 58 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 HC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58HC2_S33_R1_001.fastq.gz,fastq,3711237069.0,37217240.0,webin reads 58 HC2,0:99.72,A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762,99,,,,1070592288,757099665,780689044,1102575310,280762,ERX13237785,ERS21098728,ERA30883748,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19100,ERR13828836,ERX13231602,ERS21098712,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48AC2 S17 R1 001.fastq.gz,48 AC2,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 AC2,webin reads 48 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 AC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48AC2_S17_R1_001.fastq.gz,fastq,3205206588.0,32424632.0,webin reads 48 AC2,0:98.85,A:902438127;C:672433401;G:694813369;T:935445436;N:76255,98,,,,902438127,672433401,694813369,935445436,76255,ERX13231602,ERS21098712,ERA30883343,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19101,ERR13835004,ERX13237770,ERS21098725,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC3 S30 R1 001.fastq.gz,58 AC3,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 AC3,webin reads 58 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC3_S30_R1_001.fastq.gz,fastq,3782993133.0,38295959.0,webin reads 58 AC3,0:98.78,A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531,98,,,,1080745150,779903026,803258485,1118994941,91531,ERX13237770,ERS21098725,ERA30883697,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System