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
5026,ERR1706529,ERX1776763,ERS1227000,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 C9,SAMEA4055890,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000051|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055890|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:24:00Z|INSDC status:public|Submitter Id:d7b0b9c0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7b0b9c0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#23,17117131,Illumina sequencing of library 17117131  constructed from sample accession ERS1227000 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence ACTGAT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#23.cram,cram,743861850.0,4959079.0,SC RUN 20417 1#23,0:75 1:75,A:188550455;C:183533703;G:184197810;T:187506925;N:72957,75,75,,,188550455,183533703,184197810,187506925,72957,ERX1776763,ERS1227000,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96302,0.96531,0.19802,0.19492,0.73298,0.73312,0.57888,0.58087,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5029,ERR1706526,ERX1776760,ERS1226955,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 C1,SAMEA4055845,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000048|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055845|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:23:08Z|INSDC status:public|Submitter Id:d799d660 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d799d660 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#20,17117095,Illumina sequencing of library 17117095  constructed from sample accession ERS1226955 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence GTTTCG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#20.cram,cram,1202223750.0,8014825.0,SC RUN 20417 1#20,0:75 1:75,A:288569721;C:312339594;G:312724314;T:288471735;N:118386,75,75,,,288569721,312339594,312724314,288471735,118386,ERX1776760,ERS1226955,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9701,0.97208,0.23493,0.2308,0.75856,0.75893,0.51831,0.52827,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5033,ERR1706522,ERX1776756,ERS1226910,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B6,SAMEA4055800,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000044|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055800|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:20Z|INSDC status:public|Submitter Id:d778e0e0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d778e0e0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#16,17117142,Illumina sequencing of library 17117142  constructed from sample accession ERS1226910 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence CCGTCC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#16.cram,cram,1397786700.0,9318578.0,SC RUN 20417 1#16,0:75 1:75,A:370541493;C:328697895;G:330649047;T:367761875;N:136390,75,75,,,370541493,328697895,330649047,367761875,136390,ERX1776756,ERS1226910,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95779,0.96097,0.15701,0.15529,0.72462,0.72425,0.53437,0.53651,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5034,ERR1706521,ERX1776755,ERS1226903,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B4,SAMEA4055793,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000043|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055793|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:11Z|INSDC status:public|Submitter Id:d7713fc0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7713fc0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#15,17117130,Illumina sequencing of library 17117130  constructed from sample accession ERS1226903 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence ATGTCA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#15.cram,cram,2090642550.0,13937617.0,SC RUN 20417 1#15,0:75 1:75,A:573574606;C:473115476;G:474137164;T:569607223;N:208081,75,75,,,573574606,473115476,474137164,569607223,208081,ERX1776755,ERS1226903,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95314,0.95602,0.13917,0.13779,0.71605,0.7161,0.5009,0.49877,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5035,ERR1706520,ERX1776754,ERS1226896,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B3,SAMEA4055786,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000042|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055786|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:03Z|INSDC status:public|Submitter Id:d7697790 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7697790 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#14,17117118,Illumina sequencing of library 17117118  constructed from sample accession ERS1226896 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence AGTTCC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#14.cram,cram,1829182200.0,12194548.0,SC RUN 20417 1#14,0:75 1:75,A:501496169;C:412501773;G:416194477;T:498811651;N:178130,75,75,,,501496169,412501773,416194477,498811651,178130,ERX1776754,ERS1226896,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95118,0.95498,0.14818,0.14602,0.71431,0.71478,0.49278,0.4993,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5036,ERR1706519,ERX1776753,ERS1226884,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B2,SAMEA4055774,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000041|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055774|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:52Z|INSDC status:public|Submitter Id:d761fd80 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d761fd80 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#13,17117106,Illumina sequencing of library 17117106  constructed from sample accession ERS1226884 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence AGTCAA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#13.cram,cram,969474450.0,6463163.0,SC RUN 20417 1#13,0:75 1:75,A:262909712;C:222419636;G:222543360;T:261505885;N:95857,75,75,,,262909712,222419636,222543360,261505885,95857,ERX1776753,ERS1226884,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95449,0.95866,0.15114,0.14937,0.71437,0.71465,0.51271,0.50858,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5037,ERR1706518,ERX1776752,ERS1226870,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B1,SAMEA4055760,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000040|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055760|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:36Z|INSDC status:public|Submitter Id:d75a3550 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d75a3550 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#12,17117094,Illumina sequencing of library 17117094  constructed from sample accession ERS1226870 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence CTTGTA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#12.cram,cram,1454862600.0,9699084.0,SC RUN 20417 1#12,0:75 1:75,A:398496982;C:328471618;G:330736633;T:397014742;N:142625,75,75,,,398496982,328471618,330736633,397014742,142625,ERX1776752,ERS1226870,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95557,0.95961,0.13233,0.1312,0.71441,0.71488,0.49023,0.48445,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5038,ERR1706517,ERX1776751,ERS1226860,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A12,SAMEA4055750,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000039|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055750|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:28Z|INSDC status:public|Submitter Id:d7529430 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7529430 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#11,17117082,Illumina sequencing of library 17117082  constructed from sample accession ERS1226860 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence GGCTAC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#11.cram,cram,1746393900.0,11642626.0,SC RUN 20417 1#11,0:75 1:75,A:431979433;C:441330253;G:441743262;T:431172392;N:168560,75,75,,,431979433,441330253,441743262,431172392,168560,ERX1776751,ERS1226860,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96506,0.9668,0.22176,0.21891,0.74491,0.74621,0.60192,0.59716,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5039,ERR1706516,ERX1776750,ERS1226849,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A11,SAMEA4055739,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000038|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055739|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:18Z|INSDC status:public|Submitter Id:d74a56d0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d74a56d0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#10,17117070,Illumina sequencing of library 17117070  constructed from sample accession ERS1226849 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence TAGCTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#10.cram,cram,1489471050.0,9929807.0,SC RUN 20417 1#10,0:75 1:75,A:370582953;C:374410965;G:374249460;T:370079632;N:148040,75,75,,,370582953,374410965,374249460,370079632,148040,ERX1776750,ERS1226849,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96529,0.96757,0.21607,0.21231,0.74272,0.7432,0.59703,0.6019,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5040,ERR1706515,ERX1776749,ERS1226835,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A9,SAMEA4055725,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055725|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:06Z|INSDC status:public|Submitter Id:d7428ea0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7428ea0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#9,17117058,Illumina sequencing of library 17117058  constructed from sample accession ERS1226835 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence GATCAG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#9.cram,cram,812740200.0,5418268.0,SC RUN 20417 1#9,0:75 1:75,A:212802181;C:193901585;G:194345487;T:211612018;N:78929,75,75,,,212802181,193901585,194345487,211612018,78929,ERX1776749,ERS1226835,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95783,0.95996,0.17262,0.1685,0.72413,0.72448,0.53944,0.53954,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5041,ERR1706514,ERX1776748,ERS1226824,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A8,SAMEA4055714,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000036|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055714|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:58Z|INSDC status:public|Submitter Id:d73ac670 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d73ac670 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#8,17117141,Illumina sequencing of library 17117141  constructed from sample accession ERS1226824 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence ACTTGA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#8.cram,cram,1782401400.0,11882676.0,SC RUN 20417 1#8,0:75 1:75,A:458909593;C:432851102;G:434061292;T:456406952;N:172461,75,75,,,458909593,432851102,434061292,456406952,172461,ERX1776748,ERS1226824,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96096,0.96367,0.18551,0.18292,0.73413,0.73373,0.56474,0.56438,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5042,ERR1706513,ERX1776747,ERS1226813,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A7,SAMEA4055703,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000035|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055703|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:49Z|INSDC status:public|Submitter Id:d7332550 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7332550 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#7,17117129,Illumina sequencing of library 17117129  constructed from sample accession ERS1226813 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence CAGATC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#7.cram,cram,396397350.0,2642649.0,SC RUN 20417 1#7,0:75 1:75,A:103468605;C:95292253;G:94558692;T:103038245;N:39555,75,75,,,103468605,95292253,94558692,103038245,39555,ERX1776747,ERS1226813,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96013,0.96276,0.17171,0.16938,0.72941,0.73046,0.54526,0.54527,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9892,ERR4172795,ERX4136409,ERS4580819,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sibling 3,SAMEA6853229,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853229|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sibling 3 p,sibling 3 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-sibs-3_S6_R1.fastq.gz UCLGNS1141-gfp-sibs-3_S6_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp sibs 3 S6 R,0:81 1:81,A:1144578958;C:1113109875;G:1138809559;T:1117038434;N:213932,81,81,,,1144578958,1113109875,1138809559,1117038434,213932,ERX4136409,ERS4580819,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96684,0.96492,0.03244,0.0317,0.71236,0.71514,0.45871,0.46189,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9893,ERR4172794,ERX4136408,ERS4580818,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sibling 2,SAMEA6853228,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853228|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sibling 2 p,sibling 2 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-sibs-2_S4_R1.fastq.gz UCLGNS1141-gfp-sibs-2_S4_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp sibs 2 S4 R,0:81 1:81,A:1056280368;C:1036355469;G:1045429486;T:1035773622;N:189389,81,81,,,1056280368,1036355469,1045429486,1035773622,189389,ERX4136408,ERS4580818,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.95511,0.95696,0.02941,0.02903,0.71492,0.71628,0.45765,0.46537,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9894,ERR4172793,ERX4136407,ERS4580817,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sibling 1,SAMEA6853227,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853227|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sibling 1 p,sibling 1 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-sibs-1_S2_R1.fastq.gz UCLGNS1141-gfp-sibs-1_S2_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp sibs 1 S2 R,0:81 1:81,A:1121176859;C:1093927654;G:1108608188;T:1101082277;N:209264,81,81,,,1121176859,1093927654,1108608188,1101082277,209264,ERX4136407,ERS4580817,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.95795,0.96004,0.02885,0.02854,0.71648,0.71756,0.44348,0.43956,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9895,ERR4172792,ERX4136406,ERS4580816,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sfpq 3,SAMEA6853226,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853226|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sfpq 3 p,sfpq 3 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-neg_3_S5_R1.fastq.gz UCLGNS1141-gfp-neg_3_S5_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp neg 3 S5 R,0:81 1:81,A:845849249;C:772302798;G:911660213;T:787409272;N:154042,81,81,,,845849249,772302798,911660213,787409272,154042,ERX4136406,ERS4580816,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96298,0.95486,0.03415,0.03476,0.7167,0.73503,0.4665,0.45947,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9896,ERR4172791,ERX4136405,ERS4580815,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sfpq 2,SAMEA6853225,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853225|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sfpq 2 p,sfpq 2 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-neg-2_S3_R1.fastq.gz UCLGNS1141-gfp-neg-2_S3_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp neg 2 S3 R,0:81 1:81,A:961156886;C:917011292;G:942713581;T:936109877;N:157724,81,81,,,961156886,917011292,942713581,936109877,157724,ERX4136405,ERS4580815,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96276,0.96147,0.03436,0.03382,0.71892,0.72021,0.4581,0.46402,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
9897,ERR4172790,ERX4136404,ERS4580814,ERP121885,PRJEB38455,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9113,Transcriptome Analysis,RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,sfpq 1,SAMEA6853224,Centre for Developmental Neurobiology King's College London,ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853224|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9113:sfpq 1 p,sfpq 1 p,RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121885,Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19,UCLGNS1141-gfp-neg-1_S1_R1.fastq.gz UCLGNS1141-gfp-neg-1_S1_R2.fastq.gz,fastq fastq,,,E MTAB 9113:UCLGNS1141 gfp neg 1 S1 R,0:81 1:81,A:1046317524;C:1014946275;G:1036910299;T:1023619857;N:185237,81,81,,,1046317524,1014946275,1036910299,1023619857,185237,ERX4136404,ERS4580814,ERA2625401,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,2,0.96015,0.96173,0.03114,0.03098,0.7175,0.71865,0.46666,0.46399,81,81,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2020-05-22,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures
10141,ERR4973564,ERX4792138,ERS5459722,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 3,SAMEA7703213,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703213|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 3,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 3 s,sibling 3 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,70_AACCGA_70_ACTAGC_S2_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 3,0:76 1:0,A:385382600;C:210104151;G:238678838;T:315495923;N:5536,76,0,,,385382600,210104151,238678838,315495923,5536,ERX4792138,ERS5459722,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82613,,0.13111,,0.77597,,0.53833,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10142,ERR4973563,ERX4792137,ERS5459721,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 2,SAMEA7703212,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703212|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 2,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 2 s,sibling 2 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,69_AGTTGA_69_CTTACA_S7_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 2,0:76 1:0,A:405337161;C:226099266;G:255734601;T:341120121;N:5955,76,0,,,405337161,226099266,255734601,341120121,5955,ERX4792137,ERS5459721,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.84066,,0.12241,,0.77755,,0.56472,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10143,ERR4973562,ERX4792136,ERS5459720,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 1,SAMEA7703211,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703211|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 1,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 1 s,sibling 1 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,68_CCAATT_68_GTCCCG_S11_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 1,0:76 1:0,A:440539801;C:236835299;G:268057277;T:355636994;N:6169,76,0,,,440539801,236835299,268057277,355636994,6169,ERX4792136,ERS5459720,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82002,,0.12908,,0.77766,,0.54981,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10144,ERR4973561,ERX4792135,ERS5459719,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 3,SAMEA7703210,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703210|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 3,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 3 s,sfpq 3 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,67_TCGTTC_67_TGCTAT_S22_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 3,0:76 1:0,A:493165327;C:268347233;G:303443918;T:399152596;N:7138,76,0,,,493165327,268347233,303443918,399152596,7138,ERX4792135,ERS5459719,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82521,,0.12349,,0.78545,,0.57446,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10145,ERR4973560,ERX4792134,ERS5459718,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 2,SAMEA7703209,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703209|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 2,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 2 s,sfpq 2 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,66_GACGAT_66_TCAGTC_S18_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 2,0:76 1:0,A:426637005;C:227027693;G:257342561;T:338159540;N:5909,76,0,,,426637005,227027693,257342561,338159540,5909,ERX4792134,ERS5459718,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.81933,,0.11571,,0.78593,,0.56675,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10146,ERR4973559,ERX4792133,ERS5459717,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 1,SAMEA7703208,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703208|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 1,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 1 s,sfpq 1 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,65_AAGCTC_65_AAGAAG_S3_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 1,0:76 1:0,A:425613638;C:225707961;G:254738302;T:336863560;N:5847,76,0,,,425613638,225707961,254738302,336863560,5847,ERX4792133,ERS5459717,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.81857,,0.11342,,0.78587,,0.56439,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11821,ERR11834690,ERX11232843,ERS16254762,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 4,SAMEA114265804,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265804|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 4|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 4|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 4 p,Sample 4 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_2.fastq.gz NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_1.fastq.gz,fastq fastq,9764006696.0,32331148.0,E MTAB 13263:NG 32417 R2113 dre C1 clobetasolpropionate lib667285 10169 3 ,0:151 1:151,A:2627275848;C:2223323771;G:2323190525;T:2590103027;N:113525,151,151,,,2627275848,2223323771,2323190525,2590103027,113525,ERX11232843,ERS16254762,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95424,0.95502,0.12596,0.12401,0.65884,0.65825,0.48134,0.48327,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11822,ERR11834689,ERX11232842,ERS16254761,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 3,SAMEA114265803,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265803|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 3|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 3|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 3 p,Sample 3 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_2.fastq.gz NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_1.fastq.gz,fastq fastq,13326663550.0,44128025.0,E MTAB 13263:NG 32417 R2112 dre nc clobetasolpropionate lib673071 10180 1 ,0:151 1:151,A:3641640344;C:3020489123;G:3072643196;T:3591659412;N:231475,151,151,,,3641640344,3020489123,3072643196,3591659412,231475,ERX11232842,ERS16254761,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95271,0.95293,0.11945,0.1151,0.65819,0.6579,0.47257,0.47803,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11823,ERR11834684,ERX11232837,ERS16254756,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 1,SAMEA114265798,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265798|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 1|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.3|sample name:E MTAB 13263:Sample 1|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 1 p,Sample 1 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_1.fastq.gz NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_2.fastq.gz,fastq fastq,10152616370.0,33617935.0,E MTAB 13263:NG 32417 R2110 dre nc clobetasolpropionate lib667282 10169 3 ,0:151 1:151,A:2743478864;C:2319134955;G:2378048842;T:2711839167;N:114542,151,151,,,2743478864,2319134955,2378048842,2711839167,114542,ERX11232837,ERS16254756,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95273,0.95457,0.13567,0.13174,0.65896,0.65841,0.47947,0.47815,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11824,ERR11834691,ERX11232844,ERS16254763,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 5,SAMEA114265805,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265805|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 5|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.2|sample name:E MTAB 13263:Sample 5|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 5 p,Sample 5 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_1.fastq.gz NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_2.fastq.gz,fastq fastq,11690304334.0,38709617.0,E MTAB 13263:NG 32417 R2114 dre C1 clobetasolpropionate lib667286 10169 3 ,0:151 1:151,A:3142106866;C:2677986743;G:2767050957;T:3103028799;N:130969,151,151,,,3142106866,2677986743,2767050957,3103028799,130969,ERX11232844,ERS16254763,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95418,0.95523,0.12548,0.12397,0.66026,0.66016,0.46767,0.47253,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11825,ERR11834688,ERX11232841,ERS16254760,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 2,SAMEA114265802,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265802|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 2|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 2|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 2 p,Sample 2 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_1.fastq.gz NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_2.fastq.gz,fastq fastq,11827163184.0,39162792.0,E MTAB 13263:NG 32417 R2111 dre nc clobetasolpropionate lib673070 10180 1 ,0:151 1:151,A:3256286612;C:2657918302;G:2701905502;T:3210846546;N:206222,151,151,,,3256286612,2657918302,2701905502,3210846546,206222,ERX11232841,ERS16254760,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95203,0.95292,0.12277,0.11772,0.66048,0.65837,0.47243,0.4729,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11826,ERR11834693,ERX11232846,ERS16254765,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 7,SAMEA114265807,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265807|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 7|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 7|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 7 p,Sample 7 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_1.fastq.gz NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_2.fastq.gz,fastq fastq,11114382784.0,36802592.0,E MTAB 13263:NG 32417 R2116 dre nc imq clobetasolpropionate lib667288 10169 3 ,0:151 1:151,A:2997376944;C:2547742011;G:2613273908;T:2955864850;N:125071,151,151,,,2997376944,2547742011,2613273908,2955864850,125071,ERX11232846,ERS16254765,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95392,0.9539,0.12951,0.12707,0.65628,0.65731,0.48132,0.48179,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11827,ERR11834695,ERX11232848,ERS16254767,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 9,SAMEA114265809,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265809|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 9|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.9|sample name:E MTAB 13263:Sample 9|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 9 p,Sample 9 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_1.fastq.gz NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_2.fastq.gz,fastq fastq,9422294300.0,31199650.0,E MTAB 13263:NG 32417 R2118 dre nc imq clobetasolpropionate lib667290 10169 3 ,0:151 1:151,A:2541445212;C:2157798531;G:2214381344;T:2508560588;N:108625,151,151,,,2541445212,2157798531,2214381344,2508560588,108625,ERX11232848,ERS16254767,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95337,0.95433,0.13046,0.12718,0.65845,0.65815,0.48198,0.48414,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11828,ERR11834687,ERX11232840,ERS16254759,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 12,SAMEA114265801,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265801|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 12|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 12|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 12 p,Sample 12 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_2.fastq.gz NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_1.fastq.gz,fastq fastq,9285032280.0,30745140.0,E MTAB 13263:NG 32417 R2121 dre C1 imq clobetasolpropionate lib667293 10169 3 ,0:151 1:151,A:2504765552;C:2110325477;G:2196928032;T:2472905759;N:107460,151,151,,,2504765552,2110325477,2196928032,2472905759,107460,ERX11232840,ERS16254759,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95411,0.95451,0.12502,0.12228,0.65829,0.65774,0.48259,0.47946,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11829,ERR11834694,ERX11232847,ERS16254766,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 8,SAMEA114265808,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265808|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 8|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.5|sample name:E MTAB 13263:Sample 8|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 8 p,Sample 8 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_1.fastq.gz NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_2.fastq.gz,fastq fastq,10247527118.0,33932209.0,E MTAB 13263:NG 32417 R2117 dre nc imq clobetasolpropionate lib667289 10169 3 ,0:151 1:151,A:2766675319;C:2342307825;G:2405294253;T:2733131648;N:118073,151,151,,,2766675319,2342307825,2405294253,2733131648,118073,ERX11232847,ERS16254766,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.9541,0.95434,0.13364,0.13098,0.6576,0.6565,0.48068,0.48029,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11830,ERR11834692,ERX11232845,ERS16254764,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 6,SAMEA114265806,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265806|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 6|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 6|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 6 p,Sample 6 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_1.fastq.gz NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_2.fastq.gz,fastq fastq,10440673634.0,34571767.0,E MTAB 13263:NG 32417 R2115 dre C1 clobetasolpropionate lib667287 10169 3 ,0:151 1:151,A:2805459166;C:2397120759;G:2463616298;T:2774359989;N:117422,151,151,,,2805459166,2397120759,2463616298,2774359989,117422,ERX11232845,ERS16254764,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95568,0.9548,0.13056,0.12563,0.65882,0.66332,0.49162,0.48586,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11831,ERR11834685,ERX11232838,ERS16254757,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 10,SAMEA114265799,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265799|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 10|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 10|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 10 p,Sample 10 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_2.fastq.gz NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_1.fastq.gz,fastq fastq,11267068246.0,37308173.0,E MTAB 13263:NG 32417 R2119 dre C1 imq clobetasolpropionate lib667291 10169 3 ,0:151 1:151,A:3042432765;C:2574394239;G:2642086000;T:3008026288;N:128954,151,151,,,3042432765,2574394239,2642086000,3008026288,128954,ERX11232838,ERS16254757,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95345,0.95411,0.13324,0.13062,0.65796,0.65892,0.48176,0.48174,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11832,ERR11834686,ERX11232839,ERS16254758,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 11,SAMEA114265800,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265800|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 11|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 11|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 11 p,Sample 11 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. 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.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_2.fastq.gz NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_1.fastq.gz,fastq fastq,9922486330.0,32855915.0,E MTAB 13263:NG 32417 R2120 dre C1 imq clobetasolpropionate lib667292 10169 3 ,0:151 1:151,A:2673462020;C:2268840894;G:2345658284;T:2634411815;N:113317,151,151,,,2673462020,2268840894,2345658284,2634411815,113317,ERX11232839,ERS16254758,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.9551,0.95621,0.1193,0.11675,0.65833,0.65827,0.48596,0.48547,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
26016,SRR25868588,SRX21589851,SRS18767424,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T5VAa5,,strain:AB wild type|age:24 hpf 120 hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 55876|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:5|dose:0|dose units:ug/L|treatment:VehicleControl|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo control,T5VAa5 S217,T5VAa5 S217,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T5VAa5_S217_L002_R1_001.fastq.gz T5VAa5_S217_L002_R2_001.fastq.gz,fastq fastq,8100529500.0,27001765.0,T5VAa5 S217 L002 R1 001.fastq.gz,0:150 1:150,A:2094646242;C:1839873833;G:2144213073;T:2021734883;N:61469,150,150,,,2094646242,1839873833,2144213073,2021734883,61469,SRX21589851,SRS18767424,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.61505,0.62102,0.08204,0.08402,0.72581,0.72545,0.499,0.50086,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Multi-stage,Multi-stage,Trunk,Surface Structure
29041,SRR26990794,SRX22683825,SRS19677539,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut3,GSM7924158,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924158,GSM7924158: WT gut3; Danio rerio; RNA Seq,GSM7924158 r1,GSM7924158,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz,fastq fastq,6066709786.0,20088443.0,GSM7924158 r1,0:151 1:151,A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156,151,151,,,1673762656,1360901090,1385125931,1646863953,56156,SRX22683825,SRS19677539,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92515,0.9297,0.0691,0.0659,0.75041,0.75022,0.53007,0.53064,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29042,SRR26990795,SRX22683824,SRS19677538,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut2,GSM7924157,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924157,GSM7924157: WT gut2; Danio rerio; RNA Seq,GSM7924157 r1,GSM7924157,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz,fastq fastq,5406867570.0,17903535.0,GSM7924157 r1,0:151 1:151,A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612,151,151,,,1464846243,1237183908,1259215309,1445572498,49612,SRX22683824,SRS19677538,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93795,0.94322,0.05952,0.05592,0.75933,0.75887,0.54179,0.53451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29043,SRR26990796,SRX22683823,SRS19677537,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut1,GSM7924156,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924156,GSM7924156: WT gut1; Danio rerio; RNA Seq,GSM7924156 r1,GSM7924156,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz,fastq fastq,5162192908.0,17093354.0,GSM7924156 r1,0:151 1:151,A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343,151,151,,,1404682153,1175657030,1196829496,1384975886,48343,SRX22683823,SRS19677537,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93119,0.93585,0.06122,0.05809,0.74757,0.74757,0.54124,0.54417,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29044,SRR26990797,SRX22683822,SRS19677536,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut3,GSM7924155,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924155,GSM7924155: itgavKO gut3; Danio rerio; RNA Seq,GSM7924155 r1,GSM7924155,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz,fastq fastq,4146743578.0,13730939.0,GSM7924155 r1,0:151 1:151,A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387,151,151,,,1130002132,943522869,958031732,1115146458,40387,SRX22683822,SRS19677536,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93764,0.94144,0.05938,0.05594,0.7553,0.75485,0.55535,0.55018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29045,SRR26990798,SRX22683821,SRS19677535,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut2,GSM7924154,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924154,GSM7924154: itgavKO gut2; Danio rerio; RNA Seq,GSM7924154 r1,GSM7924154,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz,fastq fastq,4225756140.0,13992570.0,GSM7924154 r1,0:151 1:151,A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530,151,151,,,1133211420,974497998,995876972,1122129220,40530,SRX22683821,SRS19677535,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.95341,0.95884,0.05109,0.04883,0.77542,0.77368,0.51301,0.50704,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29046,SRR26990799,SRX22683820,SRS19677534,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itagvKO gut1,GSM7924153,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itagvKO gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924153,GSM7924153: itagvKO gut1; Danio rerio; RNA Seq,GSM7924153 r1,GSM7924153,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz,fastq fastq,5954117844.0,19715622.0,GSM7924153 r1,0:151 1:151,A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859,151,151,,,1600496071,1372939932,1393534700,1587094282,52859,SRX22683820,SRS19677534,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94807,0.95298,0.05682,0.05385,0.74004,0.73925,0.54423,0.54484,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29047,SRR26990800,SRX22683819,SRS19677533,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT brain 3,GSM7924152,,source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT brain 3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,brain,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:brain|genotype:wildtype|time:50dpf,GSM7924152,GSM7924152: WT brain 3; Danio rerio; RNA Seq,GSM7924152 r1,GSM7924152,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,6_WT_3B_S21_L001_R2_001.fastq.gz 6_WT_3B_S21_L001_R1_001.fastq.gz,fastq fastq,4461174200.0,14772100.0,GSM7924152 r1,0:151 1:151,A:1278513355;C:956242646;G:972856171;T:1253520960;N:41068,151,151,,,1278513355,956242646,972856171,1253520960,41068,SRX22683819,SRS19677533,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93808,0.93817,0.14984,0.14408,0.70388,0.7035,0.49899,0.49333,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Brain,Nervous System
29048,SRR26990801,SRX22683818,SRS19677532,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT brain 2,GSM7924151,,source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT brain 2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,brain,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:brain|genotype:wildtype|time:50dpf,GSM7924151,GSM7924151: WT brain 2; Danio rerio; RNA Seq,GSM7924151 r1,GSM7924151,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,5_WT_2B_S20_L001_R2_001.fastq.gz 5_WT_2B_S20_L001_R1_001.fastq.gz,fastq fastq,4801957946.0,15900523.0,GSM7924151 r1,0:151 1:151,A:1362644269;C:1038749357;G:1059777543;T:1340744881;N:41896,151,151,,,1362644269,1038749357,1059777543,1340744881,41896,SRX22683818,SRS19677532,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.9395,0.94022,0.14136,0.13794,0.70853,0.70845,0.48158,0.51366,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Brain,Nervous System
29049,SRR26990802,SRX22683817,SRS19677531,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT brain 1,GSM7924150,,source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT brain 1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,brain,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:brain|genotype:wildtype|time:50dpf,GSM7924150,GSM7924150: WT brain 1; Danio rerio; RNA Seq,GSM7924150 r1,GSM7924150,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,4_WT_1B_S19_L001_R1_001.fastq.gz 4_WT_1B_S19_L001_R2_001.fastq.gz,fastq fastq,1712568916.0,5670758.0,GSM7924150 r1,0:151 1:151,A:496576572;C:361494257;G:367701092;T:486774148;N:22847,151,151,,,496576572,361494257,367701092,486774148,22847,SRX22683817,SRS19677531,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92654,0.92757,0.14818,0.14172,0.71394,0.7122,0.5011,0.50084,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Brain,Nervous System
29050,SRR26990803,SRX22683816,SRS19677530,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO brain 3,GSM7924149,,source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO brain 3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,brain,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:brain|genotype:itgavKO mutant|time:50dpf,GSM7924149,GSM7924149: itgavKO brain 3; Danio rerio; RNA Seq,GSM7924149 r1,GSM7924149,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,3_itgavKO_3B_S18_L001_R2_001.fastq.gz 3_itgavKO_3B_S18_L001_R1_001.fastq.gz,fastq fastq,3079420614.0,10196757.0,GSM7924149 r1,0:151 1:151,A:869781292;C:673463468;G:684386550;T:851761331;N:27973,151,151,,,869781292,673463468,684386550,851761331,27973,SRX22683816,SRS19677530,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94057,0.94157,0.13371,0.12847,0.70429,0.70451,0.49726,0.49861,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Brain,Nervous System
29051,SRR26990804,SRX22683815,SRS19677529,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO brain 2,GSM7924148,,source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO brain 2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,brain,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:brain|genotype:itgavKO mutant|time:50dpf,GSM7924148,GSM7924148: itgavKO brain 2; Danio rerio; RNA Seq,GSM7924148 r1,GSM7924148,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,2_itgavKO_2B_S17_L001_R1_001.fastq.gz 2_itgavKO_2B_S17_L001_R2_001.fastq.gz,fastq fastq,1913701218.0,6336759.0,GSM7924148 r1,0:151 1:151,A:549324781;C:410519448;G:417112515;T:536726028;N:18446,151,151,,,549324781,410519448,417112515,536726028,18446,SRX22683815,SRS19677529,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93075,0.93209,0.15174,0.14613,0.70449,0.70475,0.48199,0.48317,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Brain,Nervous System
29052,SRR26990805,SRX22683814,SRS19677528,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO brain 1,GSM7924147,,source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO brain 1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,brain,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:brain|genotype:itgavKO mutant|time:50dpf,GSM7924147,GSM7924147: itgavKO brain 1; Danio rerio; RNA Seq,GSM7924147 r1,GSM7924147,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,1_itgavKO_1B_S16_L001_R1_001.fastq.gz 1_itgavKO_1B_S16_L001_R2_001.fastq.gz,fastq fastq,2056389876.0,6809238.0,GSM7924147 r1,0:151 1:151,A:593258034;C:437927433;G:446814957;T:578370581;N:18871,151,151,,,593258034,437927433,446814957,578370581,18871,SRX22683814,SRS19677528,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93156,0.93304,0.1488,0.14352,0.70224,0.70293,0.49609,0.49296,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Brain,Nervous System
29053,SRR26990806,SRX22683813,SRS19677527,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish itgavko tc 8d 3,GSM7924146,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing,zebrafish itgavko tc 8d 3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf,GSM7924146,GSM7924146: zebrafish itgavko tc 8d 3; Danio rerio; RNA Seq,GSM7924146 r1,GSM7924146,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,6_zebrafish_itgavko_tc_8d_3_S31_L001_R2_001.fastq.gz 6_zebrafish_itgavko_tc_8d_3_S31_L001_R1_001.fastq.gz,fastq fastq,3875161320.0,12831660.0,GSM7924146 r1,0:151 1:151,A:1223303253;C:711567515;G:746979670;T:1193309732;N:1150,151,151,,,1223303253,711567515,746979670,1193309732,1150,SRX22683813,SRS19677527,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.84595,0.84551,0.30568,0.30506,0.77329,0.76948,0.63885,0.64046,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29054,SRR26990807,SRX22683812,SRS19677526,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish itgavko tc 8d 2,GSM7924145,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing,zebrafish itgavko tc 8d 2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf,GSM7924145,GSM7924145: zebrafish itgavko tc 8d 2; Danio rerio; RNA Seq,GSM7924145 r1,GSM7924145,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,5_zebrafish_itgavko_tc_8d_2_S30_L001_R1_001.fastq.gz 5_zebrafish_itgavko_tc_8d_2_S30_L001_R2_001.fastq.gz,fastq fastq,4365991652.0,14456926.0,GSM7924145 r1,0:151 1:151,A:1270600077;C:909032449;G:940039197;T:1246318704;N:1225,151,151,,,1270600077,909032449,940039197,1246318704,1225,SRX22683812,SRS19677526,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.91871,0.91856,0.21085,0.20755,0.71114,0.70873,0.45669,0.45984,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29055,SRR26990808,SRX22683811,SRS19677525,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish itgavko tc 8d 1,GSM7924144,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing,zebrafish itgavko tc 8d 1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf,GSM7924144,GSM7924144: zebrafish itgavko tc 8d 1; Danio rerio; RNA Seq,GSM7924144 r1,GSM7924144,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,4_zebrafish_itgavko_tc_8d_1_S29_L001_R1_001.fastq.gz 4_zebrafish_itgavko_tc_8d_1_S29_L001_R2_001.fastq.gz,fastq fastq,4802635634.0,15902767.0,GSM7924144 r1,0:151 1:151,A:1431003343;C:965403922;G:1003504713;T:1402722287;N:1369,151,151,,,1431003343,965403922,1003504713,1402722287,1369,SRX22683811,SRS19677525,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.90555,0.90464,0.24806,0.24593,0.72182,0.72007,0.46914,0.47508,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29056,SRR26990809,SRX22683810,SRS19677524,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish wt tc 8d 3,GSM7924143,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing,zebrafish wt tc 8d 3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf,GSM7924143,GSM7924143: zebrafish wt tc 8d 3; Danio rerio; RNA Seq,GSM7924143 r1,GSM7924143,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,3_zebrafish_wt_tc_8d_3_S28_L001_R1_001.fastq.gz 3_zebrafish_wt_tc_8d_3_S28_L001_R2_001.fastq.gz,fastq fastq,4510890648.0,14936724.0,GSM7924143 r1,0:151 1:151,A:1375725383;C:876879135;G:915216593;T:1343068155;N:1382,151,151,,,1375725383,876879135,915216593,1343068155,1382,SRX22683810,SRS19677524,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.87519,0.87203,0.27672,0.27432,0.74282,0.74054,0.54199,0.54873,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29057,SRR26990810,SRX22683809,SRS19677523,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish wt tc 8d 2,GSM7924142,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing,zebrafish wt tc 8d 2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf,GSM7924142,GSM7924142: zebrafish wt tc 8d 2; Danio rerio; RNA Seq,GSM7924142 r1,GSM7924142,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,2_zebrafish_wt_tc_8d_2_S27_L001_R1_001.fastq.gz 2_zebrafish_wt_tc_8d_2_S27_L001_R2_001.fastq.gz,fastq fastq,4596331280.0,15219640.0,GSM7924142 r1,0:151 1:151,A:1337992161;C:955572266;G:991264463;T:1311501025;N:1365,151,151,,,1337992161,955572266,991264463,1311501025,1365,SRX22683809,SRS19677523,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.91445,0.91384,0.21247,0.20919,0.71135,0.70893,0.46349,0.47487,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29058,SRR26990811,SRX22683808,SRS19677522,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish wt tc 8d 1,GSM7924141,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing,zebrafish wt tc 8d 1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf,GSM7924141,GSM7924141: zebrafish wt tc 8d 1; Danio rerio; RNA Seq,GSM7924141 r1,GSM7924141,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,1_zebrafish_wt_tc_8d_1_S26_L001_R2_001.fastq.gz 1_zebrafish_wt_tc_8d_1_S26_L001_R1_001.fastq.gz,fastq fastq,3796122786.0,12569943.0,GSM7924141 r1,0:151 1:151,A:1127981217;C:766135618;G:796849753;T:1105155152;N:1046,151,151,,,1127981217,766135618,796849753,1105155152,1046,SRX22683808,SRS19677522,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.9074,0.90541,0.24401,0.24217,0.7205,0.7176,0.46736,0.47258,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29059,SRR27010032,SRX22702842,SRS19695451,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr sham C3,C3,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,C3,C3,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,C3_R2_001.fastq.gz C3_R1_001.fastq.gz,fastq fastq,7226125500.0,24087085.0,C3 R1 001.fastq.gz,0:150 1:150,A:1960622478;C:1648410555;G:1694156766;T:1922924543;N:11158,150,150,,,1960622478,1648410555,1694156766,1922924543,11158,SRX22702842,SRS19695451,SRA1760882,University of York|Biology,University of York,2,0.94281,0.94259,0.11548,0.11243,0.666,0.66768,0.4931,0.49197,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29060,SRR27010033,SRX22702841,SRS19695450,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr sham C2,C2,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,C2,C2,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,C2_R1_001.fastq.gz C2_R2_001.fastq.gz,fastq fastq,5174981700.0,17249939.0,C2 R1 001.fastq.gz,0:150 1:150,A:1397754308;C:1184093732;G:1220417954;T:1372707855;N:7851,150,150,,,1397754308,1184093732,1220417954,1372707855,7851,SRX22702841,SRS19695450,SRA1760882,University of York|Biology,University of York,2,0.94447,0.94375,0.11969,0.11666,0.68885,0.68956,0.49127,0.48884,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29061,SRR27010034,SRX22702840,SRS19695449,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT irf8 sham B6,B6,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B6|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,B6,B6,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,B6_R1_001.fastq.gz B6_R2_001.fastq.gz,fastq fastq,6038798100.0,20129327.0,B6 R1 001.fastq.gz,0:150 1:150,A:1644314055;C:1369774666;G:1410590989;T:1614109292;N:9098,150,150,,,1644314055,1369774666,1410590989,1614109292,9098,SRX22702840,SRS19695449,SRA1760882,University of York|Biology,University of York,2,0.94338,0.9424,0.12398,0.12103,0.69075,0.69203,0.49627,0.49707,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29062,SRR27010035,SRX22702839,SRS19695448,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT irf8 sham B4,B4,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,B4,B4,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,B4_R1_001.fastq.gz B4_R2_001.fastq.gz,fastq fastq,4670850600.0,15569502.0,B4 R1 001.fastq.gz,0:150 1:150,A:1265811314;C:1065724201;G:1097798356;T:1241510089;N:6640,150,150,,,1265811314,1065724201,1097798356,1241510089,6640,SRX22702839,SRS19695448,SRA1760882,University of York|Biology,University of York,2,0.94547,0.94517,0.11922,0.11549,0.68968,0.69029,0.48585,0.48669,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29063,SRR27010036,SRX22702838,SRS19695446,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT irf8 sham B3,B3,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,B3,B3,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,B3_R1_001.fastq.gz B3_R2_001.fastq.gz,fastq fastq,5982538500.0,19941795.0,B3 R1 001.fastq.gz,0:150 1:150,A:1606272011;C:1379162914;G:1419047430;T:1578047050;N:9095,150,150,,,1606272011,1379162914,1419047430,1578047050,9095,SRX22702838,SRS19695446,SRA1760882,University of York|Biology,University of York,2,0.95017,0.9501,0.09939,0.09688,0.68838,0.68964,0.48756,0.49223,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29064,SRR27010037,SRX22702837,SRS19695447,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT irf8 sham B2,B2,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,B2,B2,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,B2_R2_001.fastq.gz B2_R1_001.fastq.gz,fastq fastq,5653227300.0,18844091.0,B2 R1 001.fastq.gz,0:150 1:150,A:1525579353;C:1295599509;G:1332714404;T:1499325712;N:8322,150,150,,,1525579353,1295599509,1332714404,1499325712,8322,SRX22702837,SRS19695447,SRA1760882,University of York|Biology,University of York,2,0.94379,0.89488,0.12085,0.10989,0.69004,0.69796,0.48877,0.48916,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29065,SRR27010038,SRX22702836,SRS19695445,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT scr sham A9,A9,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,A9,A9,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,A9_R1_001.fastq.gz A9_R2_001.fastq.gz,fastq fastq,5280286800.0,17600956.0,A9 R1 001.fastq.gz,0:150 1:150,A:1438789477;C:1200820278;G:1228527888;T:1412141110;N:8047,150,150,,,1438789477,1200820278,1228527888,1412141110,8047,SRX22702836,SRS19695445,SRA1760882,University of York|Biology,University of York,2,0.93991,0.93997,0.12415,0.11988,0.68043,0.68245,0.49031,0.49263,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29066,SRR27010039,SRX22702835,SRS19695444,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 transplanted visible cells G8,G8,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G8|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,G8,G8,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,G8_R1_001.fastq.gz G8_R2_001.fastq.gz,fastq fastq,6258269400.0,20860898.0,G8 R1 001.fastq.gz,0:150 1:150,A:1703536007;C:1424705894;G:1461517358;T:1668500971;N:9170,150,150,,,1703536007,1424705894,1461517358,1668500971,9170,SRX22702835,SRS19695444,SRA1760882,University of York|Biology,University of York,2,0.94463,0.94425,0.12179,0.11924,0.68383,0.68574,0.48927,0.49078,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29067,SRR27010040,SRX22702834,SRS19695443,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 transplanted visible cells G5,G5,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,G5,G5,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,G5_R2_001.fastq.gz G5_R1_001.fastq.gz,fastq fastq,8086012500.0,26953375.0,G5 R1 001.fastq.gz,0:150 1:150,A:2209424775;C:1827141351;G:1886144200;T:2163290263;N:11911,150,150,,,2209424775,1827141351,1886144200,2163290263,11911,SRX22702834,SRS19695443,SRA1760882,University of York|Biology,University of York,2,0.94005,0.94009,0.13869,0.13535,0.68874,0.68876,0.49518,0.49562,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29068,SRR27010041,SRX22702833,SRS19695442,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 transplanted visible cells G4,G4,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,G4,G4,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,G4_R2_001.fastq.gz G4_R1_001.fastq.gz,fastq fastq,11168836800.0,37229456.0,G4 R1 001.fastq.gz,0:150 1:150,A:3056935929;C:2522420915;G:2603785258;T:2985677785;N:16913,150,150,,,3056935929,2522420915,2603785258,2985677785,16913,SRX22702833,SRS19695442,SRA1760882,University of York|Biology,University of York,2,0.94154,0.94245,0.13303,0.12991,0.68298,0.68428,0.49109,0.49258,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29069,SRR27010042,SRX22702832,SRS19695441,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 transplanted visible cells G1,G1,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,G1,G1,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,G1_R1_001.fastq.gz G1_R2_001.fastq.gz,fastq fastq,6745303500.0,22484345.0,G1 R1 001.fastq.gz,0:150 1:150,A:1832990297;C:1535916761;G:1572331210;T:1804054965;N:10267,150,150,,,1832990297,1535916761,1572331210,1804054965,10267,SRX22702832,SRS19695441,SRA1760882,University of York|Biology,University of York,2,0.9424,0.94298,0.12822,0.12534,0.68775,0.68854,0.4869,0.48958,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29070,SRR27010043,SRX22702831,SRS19695440,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted non visible cells F5,F5,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,F5,F5,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,F5_R1_001.fastq.gz F5_R2_001.fastq.gz,fastq fastq,6464113800.0,21547046.0,F5 R1 001.fastq.gz,0:150 1:150,A:1773652408;C:1452872569;G:1501709404;T:1735869784;N:9635,150,150,,,1773652408,1452872569,1501709404,1735869784,9635,SRX22702831,SRS19695440,SRA1760882,University of York|Biology,University of York,2,0.93953,0.93885,0.13889,0.13589,0.68448,0.68568,0.49419,0.49486,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29071,SRR27010044,SRX22702830,SRS19695439,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted non visible cells F4,F4,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,F4,F4,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,F4_R1_001.fastq.gz F4_R2_001.fastq.gz,fastq fastq,7547491800.0,25158306.0,F4 R1 001.fastq.gz,0:150 1:150,A:2043215956;C:1726123019;G:1778767478;T:1999373636;N:11711,150,150,,,2043215956,1726123019,1778767478,1999373636,11711,SRX22702830,SRS19695439,SRA1760882,University of York|Biology,University of York,2,0.94829,0.94765,0.11775,0.11477,0.68682,0.68783,0.48624,0.49294,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29072,SRR27010045,SRX22702829,SRS19695437,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted non visible cells F3,F3,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,F3,F3,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,F3_R1_001.fastq.gz F3_R2_001.fastq.gz,fastq fastq,7796779800.0,25989266.0,F3 R1 001.fastq.gz,0:150 1:150,A:2138759764;C:1759352855;G:1808448742;T:2090206548;N:11891,150,150,,,2138759764,1759352855,1808448742,2090206548,11891,SRX22702829,SRS19695437,SRA1760882,University of York|Biology,University of York,2,0.94125,0.9421,0.13575,0.13224,0.69307,0.69469,0.4862,0.48802,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29073,SRR27010046,SRX22702828,SRS19695438,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT scr sham A4,A4,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,A4,A4,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,A4_R1_001.fastq.gz A4_R2_001.fastq.gz,fastq fastq,6954570300.0,23181901.0,A4 R1 001.fastq.gz,0:150 1:150,A:1888329109;C:1587042583;G:1627429667;T:1851758485;N:10456,150,150,,,1888329109,1587042583,1627429667,1851758485,10456,SRX22702828,SRS19695438,SRA1760882,University of York|Biology,University of York,2,0.94568,0.94593,0.11814,0.1154,0.69171,0.69161,0.49417,0.49201,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29074,SRR27010047,SRX22702827,SRS19695436,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted non visible cells F2,F2,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,F2,F2,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,F2_R2_001.fastq.gz F2_R1_001.fastq.gz,fastq fastq,7064875200.0,23549584.0,F2 R1 001.fastq.gz,0:150 1:150,A:1909747576;C:1617295332;G:1667877510;T:1869944260;N:10522,150,150,,,1909747576,1617295332,1667877510,1869944260,10522,SRX22702827,SRS19695436,SRA1760882,University of York|Biology,University of York,2,0.94737,0.94827,0.10024,0.09772,0.69057,0.69146,0.49402,0.49924,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29075,SRR27010048,SRX22702826,SRS19695435,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted visible cells E5,E5,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,E5,E5,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,E5_R1_001.fastq.gz E5_R2_001.fastq.gz,fastq fastq,9245045700.0,30816819.0,E5 R1 001.fastq.gz,0:150 1:150,A:2541240585;C:2078884464;G:2136224399;T:2488682323;N:13929,150,150,,,2541240585,2078884464,2136224399,2488682323,13929,SRX22702826,SRS19695435,SRA1760882,University of York|Biology,University of York,2,0.93981,0.93963,0.14018,0.13679,0.68544,0.68647,0.48749,0.49123,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29076,SRR27010049,SRX22702825,SRS19695434,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted visible cells E4,E4,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,E4,E4,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,E4_R1_001.fastq.gz E4_R2_001.fastq.gz,fastq fastq,9413066700.0,31376889.0,E4 R1 001.fastq.gz,0:150 1:150,A:2556541599;C:2141951710;G:2209637678;T:2504921319;N:14394,150,150,,,2556541599,2141951710,2209637678,2504921319,14394,SRX22702825,SRS19695434,SRA1760882,University of York|Biology,University of York,2,0.93966,0.94056,0.13191,0.13025,0.6845,0.68458,0.48562,0.48775,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29077,SRR27010050,SRX22702824,SRS19695433,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr transplanted visible cells E3,E3,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,E3,E3,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,E3_R1_001.fastq.gz E3_R2_001.fastq.gz,fastq fastq,7964919000.0,26549730.0,E3 R1 001.fastq.gz,0:150 1:150,A:2160541660;C:1817481684;G:1869600595;T:2117282750;N:12311,150,150,,,2160541660,1817481684,1869600595,2117282750,12311,SRX22702824,SRS19695433,SRA1760882,University of York|Biology,University of York,2,0.94418,0.94436,0.12381,0.12155,0.69043,0.69244,0.49578,0.49427,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29078,SRR27010051,SRX22702823,SRS19695432,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 sham D7,D7,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,D7,D7,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,D7_R1_001.fastq.gz D7_R2_001.fastq.gz,fastq fastq,9187165200.0,30623884.0,D7 R1 001.fastq.gz,0:150 1:150,A:2491532789;C:2097618431;G:2151100077;T:2446900236;N:13667,150,150,,,2491532789,2097618431,2151100077,2446900236,13667,SRX22702823,SRS19695432,SRA1760882,University of York|Biology,University of York,2,0.94299,0.94212,0.11906,0.11545,0.68306,0.68548,0.49177,0.49121,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29079,SRR27010052,SRX22702822,SRS19695430,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 sham D6,D6,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D6|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,D6,D6,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,D6_R1_001.fastq.gz D6_R2_001.fastq.gz,fastq fastq,5879800500.0,19599335.0,D6 R1 001.fastq.gz,0:150 1:150,A:1605109827;C:1329412433;G:1368575434;T:1576693845;N:8961,150,150,,,1605109827,1329412433,1368575434,1576693845,8961,SRX22702822,SRS19695430,SRA1760882,University of York|Biology,University of York,2,0.94062,0.94076,0.12643,0.12267,0.67959,0.68079,0.4953,0.49028,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29080,SRR27010053,SRX22702821,SRS19695431,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 sham D5,D5,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,D5,D5,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,D5_R1_001.fastq.gz D5_R2_001.fastq.gz,fastq fastq,6561881400.0,21872938.0,D5 R1 001.fastq.gz,0:150 1:150,A:1784761040;C:1494553700;G:1531680450;T:1750875924;N:10286,150,150,,,1784761040,1494553700,1531680450,1750875924,10286,SRX22702821,SRS19695431,SRA1760882,University of York|Biology,University of York,2,0.94309,0.94372,0.12249,0.11939,0.6896,0.69126,0.4916,0.48496,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29081,SRR27010054,SRX22702820,SRS19695429,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 irf8 sham D2,D2,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,D2,D2,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,D2_R1_001.fastq.gz D2_R2_001.fastq.gz,fastq fastq,6654501900.0,22181673.0,D2 R1 001.fastq.gz,0:150 1:150,A:1814773421;C:1511191953;G:1552895235;T:1775631113;N:10178,150,150,,,1814773421,1511191953,1552895235,1775631113,10178,SRX22702820,SRS19695429,SRA1760882,University of York|Biology,University of York,2,0.94117,0.94183,0.13042,0.12757,0.68578,0.68747,0.49634,0.49724,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29082,SRR27010055,SRX22702819,SRS19695428,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr sham C5,C5,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,C5,C5,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,C5_R2_001.fastq.gz C5_R1_001.fastq.gz,fastq fastq,6839917500.0,22799725.0,C5 R1 001.fastq.gz,0:150 1:150,A:1862202751;C:1544536021;G:1599909841;T:1833258970;N:9917,150,150,,,1862202751,1544536021,1599909841,1833258970,9917,SRX22702819,SRS19695428,SRA1760882,University of York|Biology,University of York,2,0.94311,0.9429,0.12484,0.12074,0.68899,0.69077,0.49108,0.49366,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29083,SRR27010056,SRX22702818,SRS19695427,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,rnaset2 scr sham C4,C4,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,C4,C4,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,C4_R1_001.fastq.gz C4_R2_001.fastq.gz,fastq fastq,6814278600.0,22714262.0,C4 R1 001.fastq.gz,0:150 1:150,A:1829280895;C:1574717969;G:1616401528;T:1793867756;N:10452,150,150,,,1829280895,1574717969,1616401528,1793867756,10452,SRX22702818,SRS19695427,SRA1760882,University of York|Biology,University of York,2,0.94942,0.95087,0.09719,0.09395,0.69445,0.69507,0.49061,0.49227,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29084,SRR27010057,SRX22702817,SRS19695425,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT scr sham A2,A2,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,A2,A2,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,A2_R1_001.fastq.gz A2_R2_001.fastq.gz,fastq fastq,9528853800.0,31762846.0,A2 R1 001.fastq.gz,0:150 1:150,A:2597197507;C:2160049241;G:2216864264;T:2554728048;N:14740,150,150,,,2597197507,2160049241,2216864264,2554728048,14740,SRX22702817,SRS19695425,SRA1760882,University of York|Biology,University of York,2,0.9445,0.94377,0.12789,0.12443,0.68414,0.68456,0.48493,0.49203,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29085,SRR27010058,SRX22702816,SRS19695426,SRP475263,PRJNA1047321,Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish,PRJNA1047321,Other,RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.,,,,WT scr sham A1,A1,,strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish: brain,A1,A1,RNA was extracted  polyA enriched  and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475263,,,A1_R1_001.fastq.gz A1_R2_001.fastq.gz,fastq fastq,7478013000.0,24926710.0,A1 R1 001.fastq.gz,0:150 1:150,A:2052485809;C:1681219485;G:1732402686;T:2011893634;N:11386,150,150,,,2052485809,1681219485,1732402686,2011893634,11386,SRX22702816,SRS19695426,SRA1760882,University of York|Biology,University of York,2,0.9395,0.93867,0.13153,0.12753,0.68933,0.691,0.4882,0.48774,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Brain,Nervous System
29175,SRR27292304,SRX22969963,SRS19936063,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  48 hours post burn,GSM7982886,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  48 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982886,GSM7982886: Burned Larval Zebrafish  48 hours post burn; Danio rerio; RNA Seq,GSM7982886 r1,GSM7982886,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz,fastq fastq,20874980529.0,178418637.0,GSM7982886 r1,0:28 1:89,A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257,28,89,,,5945091269,4392590896,4497688824,6035946283,3663257,SRX22969963,SRS19936063,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00573,0.91666,0.00222,0.19474,0.9931,0.79306,0.42082,0.53801,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29176,SRR27292305,SRX22969963,SRS19936063,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  48 hours post burn,GSM7982886,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  48 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982886,GSM7982886: Burned Larval Zebrafish  48 hours post burn; Danio rerio; RNA Seq,GSM7982886 r1,GSM7982886,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz,fastq fastq,20022973425.0,171136525.0,GSM7982886 r2,0:28 1:89,A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427,28,89,,,5709681181,4208386174,4307510275,5796282368,1113427,SRX22969963,SRS19936063,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00547,0.9154,0.00202,0.1955,0.99283,0.79423,0.39307,0.53427,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29177,SRR27292306,SRX22969962,SRS19936064,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  24 hours post burn,GSM7982885,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  24 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982885,GSM7982885: Burned Larval Zebrafish  24 hours post burn; Danio rerio; RNA Seq,GSM7982885 r1,GSM7982885,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz,fastq fastq,9782870058.0,83614274.0,GSM7982885 r1,0:28 1:89,A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140,28,89,,,2744737668,2140848416,2249400157,2645170677,2713140,SRX22969962,SRS19936064,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00752,0.92059,0.00244,0.16143,0.98944,0.82929,0.44176,0.54525,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29178,SRR27292307,SRX22969962,SRS19936064,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  24 hours post burn,GSM7982885,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  24 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982885,GSM7982885: Burned Larval Zebrafish  24 hours post burn; Danio rerio; RNA Seq,GSM7982885 r1,GSM7982885,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz,fastq fastq,9861989202.0,84290506.0,GSM7982885 r2,0:28 1:89,A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185,28,89,,,2769268861,2158644227,2263475493,2669311436,1289185,SRX22969962,SRS19936064,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.0076,0.9197,0.00232,0.16162,0.98995,0.82852,0.43786,0.55256,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29179,SRR27292308,SRX22969961,SRS19936062,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  6 hours post burn,GSM7982884,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  6 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982884,GSM7982884: Burned Larval Zebrafish  6 hours post burn; Danio rerio; RNA Seq,GSM7982884 r1,GSM7982884,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz,fastq fastq,12475938384.0,106631952.0,GSM7982884 r1,0:28 1:89,A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393,28,89,,,3401989108,2878275107,3114945415,3078525361,2203393,SRX22969961,SRS19936062,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.01053,0.89396,0.00429,0.18315,0.99458,0.85756,0.34876,0.58728,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29180,SRR27292309,SRX22969961,SRS19936062,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  6 hours post burn,GSM7982884,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  6 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982884,GSM7982884: Burned Larval Zebrafish  6 hours post burn; Danio rerio; RNA Seq,GSM7982884 r1,GSM7982884,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz,fastq fastq,11874083247.0,101487891.0,GSM7982884 r2,0:28 1:89,A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476,28,89,,,3243501055,2735412615,2958387721,2936117380,664476,SRX22969961,SRS19936062,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.01063,0.89389,0.00439,0.18047,0.99403,0.85878,0.36393,0.54831,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29181,SRR27292310,SRX22969960,SRS19936061,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  5 dpf,GSM7982883,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  5 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982883,GSM7982883: Unwounded Larval Zebrafish  5 dpf Danio rerio; RNA Seq,GSM7982883 r1,GSM7982883,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz,fastq fastq,31813158312.0,271907336.0,GSM7982883 r1,0:28 1:89,A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049,28,89,,,8991313503,6911976524,7105775004,8798521232,5572049,SRX22969960,SRS19936061,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00661,0.92343,0.00245,0.19293,0.99255,0.81379,0.35935,0.54818,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29182,SRR27292311,SRX22969960,SRS19936061,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  5 dpf,GSM7982883,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  5 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982883,GSM7982883: Unwounded Larval Zebrafish  5 dpf Danio rerio; RNA Seq,GSM7982883 r1,GSM7982883,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz,fastq fastq,30524386113.0,260892189.0,GSM7982883 r2,0:28 1:89,A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957,28,89,,,8637605077,6625244702,6807369409,8452468968,1697957,SRX22969960,SRS19936061,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00648,0.92418,0.00233,0.19549,0.99241,0.81444,0.37733,0.54674,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29183,SRR27292312,SRX22969959,SRS19936060,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  4 dpf,GSM7982882,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  4 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982882,GSM7982882: Unwounded Larval Zebrafish  4 dpf Danio rerio; RNA Seq,GSM7982882 r1,GSM7982882,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz,fastq fastq,12682286721.0,108395613.0,GSM7982882 r1,0:28 1:89,A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682,28,89,,,3575375325,2777398557,2900088646,3425909511,3514682,SRX22969959,SRS19936060,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00505,0.92112,0.00185,0.16865,0.99257,0.8258,0.38216,0.5512,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29184,SRR27292313,SRX22969959,SRS19936060,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  4 dpf,GSM7982882,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  4 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982882,GSM7982882: Unwounded Larval Zebrafish  4 dpf Danio rerio; RNA Seq,GSM7982882 r1,GSM7982882,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz,fastq fastq,12832453413.0,109679089.0,GSM7982882 r2,0:28 1:89,A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102,28,89,,,3620789787,2810897812,2929508681,3469577031,1680102,SRX22969959,SRS19936060,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.0052,0.92355,0.00192,0.16775,0.99263,0.8253,0.37089,0.55115,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29185,SRR27292314,SRX22969958,SRS19936059,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  3 dpf,GSM7982881,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  3 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982881,GSM7982881: Unwounded Larval Zebrafish  3 dpf Danio rerio; RNA Seq,GSM7982881 r1,GSM7982881,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz,fastq fastq,7586138430.0,64838790.0,GSM7982881 r1,0:28 1:89,A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816,28,89,,,2101749534,1692875352,1784872358,2005308370,1332816,SRX22969958,SRS19936059,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00976,0.92096,0.00368,0.18077,0.99356,0.83875,0.3661,0.59073,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29186,SRR27292315,SRX22969958,SRS19936059,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  3 dpf,GSM7982881,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  3 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982881,GSM7982881: Unwounded Larval Zebrafish  3 dpf Danio rerio; RNA Seq,GSM7982881 r1,GSM7982881,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz,fastq fastq,7258692168.0,62040104.0,GSM7982881 r2,0:28 1:89,A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823,28,89,,,2013529524,1617959197,1704796898,1922004726,401823,SRX22969958,SRS19936059,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00949,0.92207,0.00359,0.18081,0.99375,0.83751,0.37347,0.55889,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System