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name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9113:UCLGNS1141 gfp neg 3 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"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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sibling 3", "0:76 1:0", "A:385382600;C:210104151;G:238678838;T:315495923;N:5536", 76, 0, null, null, 385382600, 210104151, 238678838, 315495923, 5536, "ERX4792138", "ERS5459722", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.82613, null, 0.13111, null, 0.77597, null, 0.53833, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sibling 2", "0:76 1:0", "A:405337161;C:226099266;G:255734601;T:341120121;N:5955", 76, 0, null, null, 405337161, 226099266, 255734601, 341120121, 5955, "ERX4792137", "ERS5459721", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.84066, null, 0.12241, null, 0.77755, null, 0.56472, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sibling 1", "0:76 1:0", "A:440539801;C:236835299;G:268057277;T:355636994;N:6169", 76, 0, null, null, 440539801, 236835299, 268057277, 355636994, 6169, "ERX4792136", "ERS5459720", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.82002, null, 0.12908, null, 0.77766, null, 0.54981, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sfpq 3", "0:76 1:0", "A:493165327;C:268347233;G:303443918;T:399152596;N:7138", 76, 0, null, null, 493165327, 268347233, 303443918, 399152596, 7138, "ERX4792135", "ERS5459719", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.82521, null, 0.12349, null, 0.78545, null, 0.57446, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sfpq 2", "0:76 1:0", "A:426637005;C:227027693;G:257342561;T:338159540;N:5909", 76, 0, null, null, 426637005, 227027693, 257342561, 338159540, 5909, "ERX4792134", "ERS5459718", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.81933, null, 0.11571, null, 0.78593, null, 0.56675, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sfpq 1", "0:76 1:0", "A:425613638;C:225707961;G:254738302;T:336863560;N:5847", 76, 0, null, null, 425613638, 225707961, 254738302, 336863560, 5847, "ERX4792133", "ERS5459717", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.81857, null, 0.11342, null, 0.78587, null, 0.56439, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-12-10", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [10213, "ERR6511329", "ERX6138165", "ERS7264188", "ERP131213", "PRJEB46978", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159", "Other", "Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28", null, "Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs", "Zebrafish Ribodep Rep1", "SAMEA9541418", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3", "cDNA786327", "Nano3P seq", "Nano3P seq", null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP131213", "MinION sequencing", "ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28", "zebrafish_ribodep_rep1.tar.gz", "nanopore", 1745399583.0, 1644167.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3", "0:1061.57", "A:449704009;C:421915878;G:378879857;T:494899839;N:0", 1061, null, null, null, 449704009, 421915878, 378879857, 494899839, 0, "ERX6138165", "ERS7264188", "ERA5757997", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", 1, 0.01112, null, 0.0, null, 0.99997, null, 1.0, null, 546, null, "T", null, "long read", "ont", "ont", "full_length", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2023-12-28", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [10215, "ERR6511330", "ERX6138166", "ERS7264189", "ERP131213", "PRJEB46978", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159", "Other", "Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28", null, "Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs", "Zebrafish Ribodep Rep2", "SAMEA9541419", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4", "cDNA123791", "Nano3P seq", "Nano3P seq", null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP131213", "MinION sequencing", "ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28", "zebrafish_ribodep_rep2.tar.gz", "nanopore", 2038398139.0, 1955617.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4", "0:1042.33", "A:518369802;C:477535545;G:441294056;T:601198736;N:0", 1042, null, null, null, 518369802, 477535545, 441294056, 601198736, 0, "ERX6138166", "ERS7264189", "ERA5757997", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "full_length", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2023-12-28", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [10649, "ERR406885", "ERX373262", "ERS391761", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5s24", "SAMEA2299303", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299303|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.4", "batchA 24hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5s24.fq.gz", "fastq", 584550600.0, 11691012.0, "E MTAB 2194:5s24.fq.gz", "0:50 1:0", "A:154602150;C:138134763;G:138628704;T:153175234;N:9749", 50, 0, null, null, 154602150, 138134763, 138628704, 153175234, 9749, "ERX373262", "ERS391761", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.9356, null, 0.0996, null, 0.68615, null, 0.47069, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10650, "ERR406893", "ERX373261", "ERS391760", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5y32", "SAMEA2299302", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299302|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.5", "batchA 32hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5y32.fq.gz", "fastq", 528892950.0, 10577859.0, "E MTAB 2194:5y32.fq.gz", "0:50 1:0", "A:140383478;C:125036983;G:124119152;T:139344643;N:8694", 50, 0, null, null, 140383478, 125036983, 124119152, 139344643, 8694, "ERX373261", "ERS391760", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93478, null, 0.10542, null, 0.68296, null, 0.4795, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10651, "ERR406898", "ERX373260", "ERS391759", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6s24", "SAMEA2299301", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299301|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.10", "batchB 24hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6s24.fq.gz", "fastq", 542771850.0, 10855437.0, "E MTAB 2194:6s24.fq.gz", "0:50 1:0", "A:142311943;C:129686202;G:129130172;T:141634727;N:8806", 50, 0, null, null, 142311943, 129686202, 129130172, 141634727, 8806, "ERX373260", "ERS391759", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93717, null, 0.09239, null, 0.68876, null, 0.46809, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10652, "ERR406896", "ERX373259", "ERS391758", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13y32", "SAMEA2299300", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299300|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.18", "batchC 32hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13y32.fq.gz", "fastq", 649898350.0, 12997967.0, "E MTAB 2194:13y32.fq.gz", "0:50 1:0", "A:169738689;C:156130165;G:155102788;T:168916174;N:10534", 50, 0, null, null, 169738689, 156130165, 155102788, 168916174, 10534, "ERX373259", "ERS391758", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93898, null, 0.08535, null, 0.68217, null, 0.47133, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10653, "ERR406899", "ERX373258", "ERS391757", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5s32", "SAMEA2299299", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299299|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.6", "batchA 32hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5s32.fq.gz", "fastq", 566813600.0, 11336272.0, "E MTAB 2194:5s32.fq.gz", "0:50 1:0", "A:149907366;C:134421172;G:133399280;T:149076590;N:9192", 50, 0, null, null, 149907366, 134421172, 133399280, 149076590, 9192, "ERX373258", "ERS391757", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93497, null, 0.10019, null, 0.68379, null, 0.4671, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10654, "ERR406888", "ERX373257", "ERS391756", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5y24", "SAMEA2299298", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299298|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:5y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.3", "batchA 24hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5y24.fq.gz", "fastq", 578936250.0, 11578725.0, "E MTAB 2194:5y24.fq.gz", "0:50 1:0", "A:154884020;C:135497257;G:135214353;T:153331273;N:9347", 50, 0, null, null, 154884020, 135497257, 135214353, 153331273, 9347, "ERX373257", "ERS391756", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.9342, null, 0.1106, null, 0.67811, null, 0.47685, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10655, "ERR406887", "ERX373256", "ERS391755", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13s24", "SAMEA2299297", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299297|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13s24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.16", "batchC 24hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13s24.fq.gz", "fastq", 837415050.0, 16748301.0, "E MTAB 2194:13s24.fq.gz", "0:50 1:0", "A:217172462;C:202556518;G:201365353;T:216307386;N:13331", 50, 0, null, null, 217172462, 202556518, 201365353, 216307386, 13331, "ERX373256", "ERS391755", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93888, null, 0.07561, null, 0.6899, null, 0.46646, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10656, "ERR406894", "ERX373255", "ERS391754", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6y24", "SAMEA2299296", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299296|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.9", "batchB 24hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6y24.fq.gz", "fastq", 569424550.0, 11388491.0, "E MTAB 2194:6y24.fq.gz", "0:50 1:0", "A:149287318;C:136121879;G:135445765;T:148560272;N:9316", 50, 0, null, null, 149287318, 136121879, 135445765, 148560272, 9316, "ERX373255", "ERS391754", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93486, null, 0.0893, null, 0.68751, null, 0.46133, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10657, "ERR406895", "ERX373254", "ERS391753", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13s8", "SAMEA2299295", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299295|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:13s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.14", "batchC 8hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13s8.fq.gz", "fastq", 532141500.0, 10642830.0, "E MTAB 2194:13s8.fq.gz", "0:50 1:0", "A:139773245;C:127051350;G:126773752;T:138534560;N:8593", 50, 0, null, null, 139773245, 127051350, 126773752, 138534560, 8593, "ERX373254", "ERS391753", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93506, null, 0.0742, null, 0.74748, null, 0.47765, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10658, "ERR406891", "ERX373253", "ERS391752", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6s8", "SAMEA2299294", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299294|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.8", "batchB 8hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6s8.fq.gz", "fastq", 477620550.0, 9552411.0, "E MTAB 2194:6s8.fq.gz", "0:50 1:0", "A:127095393;C:112660046;G:111717464;T:126139686;N:7961", 50, 0, null, null, 127095393, 112660046, 111717464, 126139686, 7961, "ERX373253", "ERS391752", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93605, null, 0.08112, null, 0.74552, null, 0.46821, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10659, "ERR406886", "ERX373252", "ERS391751", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6y8", "SAMEA2299293", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:38Z|External Id:SAMEA2299293|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:38Z|INSDC status:public|Submitter Id:E MTAB 2194:6y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.7", "batchB 8hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6y8.fq.gz", "fastq", 508637450.0, 10172749.0, "E MTAB 2194:6y8.fq.gz", "0:50 1:0", "A:135377293;C:119833844;G:119447157;T:133970958;N:8198", 50, 0, null, null, 135377293, 119833844, 119447157, 133970958, 8198, "ERX373252", "ERS391751", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93203, null, 0.07833, null, 0.73744, null, 0.47586, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10660, "ERR406892", "ERX373251", "ERS391750", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6y32", "SAMEA2299292", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299292|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:6y32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6y32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.11", "batchB 32hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6y32.fq.gz", "fastq", 568482400.0, 11369648.0, "E MTAB 2194:6y32.fq.gz", "0:50 1:0", "A:149679881;C:135411801;G:134312216;T:149069222;N:9280", 50, 0, null, null, 149679881, 135411801, 134312216, 149069222, 9280, "ERX373251", "ERS391750", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93184, null, 0.104, null, 0.68128, null, 0.47652, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10661, "ERR406897", "ERX373250", "ERS391749", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5y8", "SAMEA2299291", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299291|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:5y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.1", "batchA 8hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5y8.fq.gz", "fastq", 497573200.0, 9951464.0, "E MTAB 2194:5y8.fq.gz", "0:50 1:0", "A:134128000;C:115688460;G:114668036;T:133080206;N:8498", 50, 0, null, null, 134128000, 115688460, 114668036, 133080206, 8498, "ERX373250", "ERS391749", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93519, null, 0.07057, null, 0.73511, null, 0.47977, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10662, "ERR406889", "ERX373249", "ERS391748", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13s32", "SAMEA2299290", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:37Z|External Id:SAMEA2299290|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:37Z|INSDC status:public|Submitter Id:E MTAB 2194:13s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.19", "batchC 32hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13s32.fq.gz", "fastq", 637724150.0, 12754483.0, "E MTAB 2194:13s32.fq.gz", "0:50 1:0", "A:165500205;C:154383334;G:152953181;T:164877160;N:10270", 50, 0, null, null, 165500205, 154383334, 152953181, 164877160, 10270, "ERX373249", "ERS391748", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93998, null, 0.08954, null, 0.68146, null, 0.4729, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10663, "ERR406890", "ERX373248", "ERS391747", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13y24", "SAMEA2299289", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299289|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:13y24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y24|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.15", "batchC 24hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:24 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13y24.fq.gz", "fastq", 834725800.0, 16694516.0, "E MTAB 2194:13y24.fq.gz", "0:50 1:0", "A:216896952;C:201332171;G:200308143;T:216174965;N:13569", 50, 0, null, null, 216896952, 201332171, 200308143, 216174965, 13569, "ERX373248", "ERS391747", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.9358, null, 0.07569, null, 0.68757, null, 0.46994, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10664, "ERR406900", "ERX373247", "ERS391746", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "13y8", "SAMEA2299288", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299288|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:13y8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:13y8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.13", "batchC 8hpf YD", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Removed yolk around 5hpf YD with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:yolk|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "13y8.fq.gz", "fastq", 457245150.0, 9144903.0, "E MTAB 2194:13y8.fq.gz", "0:50 1:0", "A:119648940;C:109589521;G:109491446;T:118507707;N:7536", 50, 0, null, null, 119648940, 109589521, 109491446, 118507707, 7536, "ERX373247", "ERS391746", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93146, null, 0.0681, null, 0.73718, null, 0.47464, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10665, "ERR406884", "ERX373246", "ERS391745", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "6s32", "SAMEA2299287", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299287|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:6s32|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:6s32|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.12", "batchB 32hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:32 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "6s32.fq.gz", "fastq", 652353200.0, 13047064.0, "E MTAB 2194:6s32.fq.gz", "0:50 1:0", "A:170844587;C:156203331;G:155264927;T:170029850;N:10505", 50, 0, null, null, 170844587, 156203331, 155264927, 170029850, 10505, "ERX373246", "ERS391745", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93785, null, 0.09102, null, 0.68554, null, 0.46397, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [10666, "ERR406901", "ERX373245", "ERS391744", "ERP004564", "PRJEB5188", "YD embryos 8 hpf 24 hpf 32 hpf", "E-MTAB-2194", "Transcriptome Analysis", "Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early life stress paradox lies developmental plasticity  a poorly understood mechanism that responds to environmental cues from early to late developmental stages.  In this study  we introduce the zebrafish Danio rerio as a model to study the early developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability  we partially remove the yolk during embryogenesis. Around 5 hpf  we removed 30% of the yolk YD samples or sham punctured embryos SP with a Hamilton syringe system. At 8  24 hpf and 32 hpf  we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.", null, null, "Protocols: Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "5s8", "SAMEA2299286", "CAS-MPG PICB", "ENA FIRST PUBLIC:2014 04 01T17:00:44Z|ENA LAST UPDATE:2018 03 08T17:04:26Z|External Id:SAMEA2299286|INSDC center name:CAS MPG PICB|INSDC first public:2014 04 01T17:00:44Z|INSDC last update:2018 03 08T17:04:26Z|INSDC status:public|Submitter Id:E MTAB 2194:5s8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|sample name:E MTAB 2194:5s8|scientific name:Danio rerio|specimen with known storage state:fresh specimen|strain:tb", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "E MTAB 2194:Unique sample ID.2", "batchA 8hpf SP", "YD embryos 8 hpf 24 hpf 32 hpf", "Zebrafish embryos in HANKS embryo buffer Around 5hpf  sham puncture the controls SP with hamilton syringe system. Trizol RNA extraction of whole embryos Truseq RNA Sample preparation Kits V2", "Experimental Factor: treatment:sham punctured embryos|Experimental Factor: time:8 hour", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP004564", "Illumina HiSeq 2000 sequencing; YD embryos 8 hpf 24 hpf 32 hpf", "ENA FIRST PUBLIC:2014 04 01|ENA LAST UPDATE:2018 11 16", "5s8.fq.gz", "fastq", 359298500.0, 7185970.0, "E MTAB 2194:5s8.fq.gz", "0:50 1:0", "A:96450828;C:83805020;G:83440885;T:95595844;N:5923", 50, 0, null, null, 96450828, 83805020, 83440885, 95595844, 5923, "ERX373245", "ERS391744", "ERA280282", "CAS-MPG PICB|ArrayExpress", "CAS-MPG PICB|ArrayExpress", 1, 0.93524, null, 0.07491, null, 0.73312, null, 0.47914, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-04-01", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11042, "ERR9839781", "ERX9385638", "ERS12199238", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish Ribodepleted RNA 2hpf  4hpf  6hpf", "Zebrafish Ribodepleted Rep3", "SAMEA110100413", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100413|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep3|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep3", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 817", "cDNA897892 ZFRDR3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA897892_ZFRDR3.tar.gz", "nanopore", 848659575.0, 587586.0, "ena RUN TAB 13 06 2022 16:07:52:808 818", "0:1444.32", "A:210205014;C:186527780;G:188214279;T:263712502;N:0", 1444, null, null, null, 210205014, 186527780, 188214279, 263712502, 0, "ERX9385638", "ERS12199238", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [11043, "ERR9839780", "ERX9385637", "ERS12199237", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish Ribodepleted RNA 2hpf  4hpf  6hpf", "Zebrafish Ribodepleted Rep2", "SAMEA110100412", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100412|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep2|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep2", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 815", "cDNA123791 ZFRDR2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA123791_ZFRDR2.tar.gz", "nanopore", 2229275175.0, 1955617.0, "ena RUN TAB 13 06 2022 16:07:52:807 816", "0:1139.93", "A:533543922;C:498938137;G:515833119;T:680959997;N:0", 1139, null, null, null, 533543922, 498938137, 515833119, 680959997, 0, "ERX9385637", "ERS12199237", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [11044, "ERR9839779", "ERX9385636", "ERS12199236", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish Ribodepleted RNA 2hpf  4hpf  6hpf", "Zebrafish Ribodepleted Rep1", "SAMEA110100411", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100411|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep1|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep1", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 813", "cDNA786327 ZFRDR1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA786327_ZFRDR1.tar.gz", "nanopore", 1900613556.0, 1660167.0, "ena RUN TAB 13 06 2022 16:07:52:807 814", "0:1144.83", "A:473050820;C:438054520;G:425169743;T:564338473;N:0", 1144, null, null, null, 473050820, 438054520, 425169743, 564338473, 0, "ERX9385636", "ERS12199236", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [11238, "ERR10782555", "ERX10233132", "ERS14439197", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 6", "E MTAB 12503:Sample 6", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 6 p", "Sample 6 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz", "fastq fastq", 14809693138.0, 49038719.0, "E MTAB 12503:20170530.A 6 R", "0:151 1:151", "A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269", 151, 151, null, null, 4069749497, 3367864217, 3430269434, 3928390721, 13419269, "ERX10233132", "ERS14439197", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.83945, 0.69977, 0.27269, 0.22488, 0.74523, 0.77654, 0.4899, 0.4358, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11239, "ERR10782554", "ERX10233131", "ERS14439196", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 5", "E MTAB 12503:Sample 5", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 5 p", "Sample 5 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz", "fastq fastq", 14954968728.0, 49519764.0, "E MTAB 12503:20170530.A 5 R", "0:151 1:151", "A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280", 151, 151, null, null, 4063340262, 3440933120, 3455723079, 3981396987, 13575280, "ERX10233131", "ERS14439196", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.85891, 0.86859, 0.28842, 0.28866, 0.7349, 0.75051, 0.45532, 0.49145, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [11242, "ERR10782551", "ERX10233128", "ERS14439193", "ERP144048", "PRJEB58983", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E-MTAB-12503", "Transcriptome Analysis", "Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, "Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Sample 7", "E MTAB 12503:Sample 7", null, "strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "E MTAB 12503:Sample 7 p", "Sample 7 p", "RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer\u00e2\u20ac\u2122s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.", "Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP144048", "Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling", "ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31", "20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz", "fastq fastq", 12726557236.0, 42140918.0, "E MTAB 12503:20170530.A 7 R", "0:151 1:151", "A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382", 151, 151, null, null, 3510176970, 2879679978, 2932244172, 3392911734, 11544382, "ERX10233128", "ERS14439193", "ERA20162442", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 2, 0.88531, 0.88678, 0.33279, 0.3329, 0.73545, 0.74992, 0.52548, 0.52864, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "sc", "unknown", "unknown", null, "Switzerland", "2023-03-31", "Multi-stage", "Embryo", "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d   Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat  purity \u2265 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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  D\u00fcren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [13299, "ERR984502", "ERX1065723", "ERS715232", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367580", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367580|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 24 sc 2286404|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTCAGCTC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 24 sc 2286404|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#24", "13741631", "Illumina sequencing of library 13741631  constructed from sample accession ERS715232 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TTCAGCTC.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#24.cram", "cram", 570705070.0, 4390039.0, "SC RUN 16164 8#24", "0:55 1:75", "A:167603013;C:88769000;G:138595187;T:175336986;N:400884", 55, 75, null, null, 167603013, 88769000, 138595187, 175336986, 400884, "ERX1065723", "ERS715232", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.18131, 0.44012, 0.12372, 0.1122, 0.96759, 0.93835, 0.63426, 0.57651, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13300, "ERR984501", "ERX1065722", "ERS715231", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367579", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367579|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 23 sc 2286403|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TACTAGTC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 23 sc 2286403|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#23", "13741630", "Illumina sequencing of library 13741630  constructed from sample accession ERS715231 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TACTAGTC.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#23.cram", "cram", 682831890.0, 5252553.0, "SC RUN 16164 8#23", "0:55 1:75", "A:201267036;C:106752351;G:152982998;T:221347859;N:481646", 55, 75, null, null, 201267036, 106752351, 152982998, 221347859, 481646, "ERX1065722", "ERS715231", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.19992, 0.5315, 0.13001, 0.13817, 0.96025, 0.92261, 0.60527, 0.55787, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13301, "ERR984500", "ERX1065721", "ERS715230", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367578", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367578|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 22 sc 2286402|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCAGATTC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 22 sc 2286402|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#22", "13741629", "Illumina sequencing of library 13741629  constructed from sample accession ERS715230 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCAGATTC.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#22.cram", "cram", 822730220.0, 6328694.0, "SC RUN 16164 8#22", "0:55 1:75", "A:241693794;C:130571512;G:177853465;T:272028770;N:582679", 55, 75, null, null, 241693794, 130571512, 177853465, 272028770, 582679, "ERX1065721", "ERS715230", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.2212, 0.54203, 0.15635, 0.13659, 0.96159, 0.9221, 0.59031, 0.55109, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13302, "ERR984499", "ERX1065720", "ERS715229", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367577", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367577|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 21 sc 2286401|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TATGCCAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 21 sc 2286401|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#21", "13741628", "Illumina sequencing of library 13741628  constructed from sample accession ERS715229 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TATGCCAG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#21.cram", "cram", 616663190.0, 4743563.0, "SC RUN 16164 8#21", "0:55 1:75", "A:176848806;C:99629161;G:137029831;T:202730142;N:425250", 55, 75, null, null, 176848806, 99629161, 137029831, 202730142, 425250, "ERX1065720", "ERS715229", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.21864, 0.57174, 0.1516, 0.14103, 0.95905, 0.9192, 0.55513, 0.51633, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13303, "ERR984498", "ERX1065719", "ERS715228", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367576", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367576|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 20 sc 2286400|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGGCTCAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 20 sc 2286400|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#20", "13741627", "Illumina sequencing of library 13741627  constructed from sample accession ERS715228 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TGGCTCAG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#20.cram", "cram", 708059950.0, 5446615.0, "SC RUN 16164 8#20", "0:55 1:75", "A:195264246;C:129715499;G:160155422;T:222438911;N:485872", 55, 75, null, null, 195264246, 129715499, 160155422, 222438911, 485872, "ERX1065719", "ERS715228", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.19642, 0.48584, 0.11921, 0.11811, 0.95422, 0.91843, 0.62494, 0.56646, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13304, "ERR984497", "ERX1065718", "ERS715227", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367575", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367575|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 19 sc 2286399|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo wild type for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCATTGAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 19 sc 2286399|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#19", "13741626", "Illumina sequencing of library 13741626  constructed from sample accession ERS715227 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCATTGAG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#19.cram", "cram", 651943890.0, 5014953.0, "SC RUN 16164 8#19", "0:55 1:75", "A:191809575;C:111573276;G:144109125;T:204007845;N:444069", 55, 75, null, null, 191809575, 111573276, 144109125, 204007845, 444069, "ERX1065718", "ERS715227", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.17909, 0.44616, 0.12326, 0.12424, 0.96256, 0.93432, 0.56606, 0.52819, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13305, "ERR984496", "ERX1065717", "ERS715226", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367574", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367574|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 18 sc 2286398|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGTATGCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 18 sc 2286398|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#18", "13741625", "Illumina sequencing of library 13741625  constructed from sample accession ERS715226 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TGTATGCG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#18.cram", "cram", 610476620.0, 4695974.0, "SC RUN 16164 8#18", "0:55 1:75", "A:181332724;C:99472616;G:132687929;T:196571397;N:411954", 55, 75, null, null, 181332724, 99472616, 132687929, 196571397, 411954, "ERX1065717", "ERS715226", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.22636, 0.55559, 0.16123, 0.16819, 0.96025, 0.92967, 0.59576, 0.54685, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13306, "ERR984495", "ERX1065716", "ERS715225", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367573", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367573|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 17 sc 2286397|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCCAGTCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 17 sc 2286397|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#17", "13741624", "Illumina sequencing of library 13741624  constructed from sample accession ERS715225 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCCAGTCG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#17.cram", "cram", 712320830.0, 5479391.0, "SC RUN 16164 8#17", "0:55 1:75", "A:204316194;C:115198795;G:158608369;T:233717227;N:480245", 55, 75, null, null, 204316194, 115198795, 158608369, 233717227, 480245, "ERX1065716", "ERS715225", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.2492, 0.59739, 0.17155, 0.14862, 0.95657, 0.92056, 0.58039, 0.53475, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13307, "ERR984494", "ERX1065715", "ERS715224", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367572", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367572|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 16 sc 2286396|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAAGTTCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 16 sc 2286396|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#16", "13741623", "Illumina sequencing of library 13741623  constructed from sample accession ERS715224 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TAAGTTCG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#16.cram", "cram", 793769340.0, 6105918.0, "SC RUN 16164 8#16", "0:55 1:75", "A:232264866;C:130235228;G:171709756;T:259013732;N:545758", 55, 75, null, null, 232264866, 130235228, 171709756, 259013732, 545758, "ERX1065715", "ERS715224", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.22065, 0.5061, 0.15274, 0.13242, 0.95779, 0.92575, 0.57619, 0.53869, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13308, "ERR984493", "ERX1065714", "ERS715223", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367571", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367571|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 15 sc 2286395|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 15 sc 2286395|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#15", "13741622", "Illumina sequencing of library 13741622  constructed from sample accession ERS715223 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCAGGAGG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#15.cram", "cram", 785479760.0, 6042152.0, "SC RUN 16164 8#15", "0:55 1:75", "A:221631721;C:150326010;G:172964474;T:240036379;N:521176", 55, 75, null, null, 221631721, 150326010, 172964474, 240036379, 521176, "ERX1065714", "ERS715223", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.26761, 0.37751, 0.19858, 0.09301, 0.95162, 0.93129, 0.56282, 0.54289, 55, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13309, "ERR984492", "ERX1065713", "ERS715222", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367570", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367570|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 14 sc 2286394|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 14 sc 2286394|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#14", "13741621", "Illumina sequencing of library 13741621  constructed from sample accession ERS715222 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCTCACGG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#14.cram", "cram", 673293530.0, 5179181.0, "SC RUN 16164 8#14", "0:55 1:75", "A:188203068;C:115934699;G:155324541;T:213374769;N:456453", 55, 75, null, null, 188203068, 115934699, 155324541, 213374769, 456453, "ERX1065713", "ERS715222", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.21855, 0.57586, 0.15197, 0.14501, 0.95946, 0.93077, 0.56453, 0.52351, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13310, "ERR984491", "ERX1065712", "ERS715221", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367569", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367569|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 13 sc 2286393|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo heterozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 13 sc 2286393|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#13", "13741620", "Illumina sequencing of library 13741620  constructed from sample accession ERS715221 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TACTTCGG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#13.cram", "cram", 783634020.0, 6027954.0, "SC RUN 16164 8#13", "0:55 1:75", "A:231435775;C:129417634;G:178939153;T:243302897;N:538561", 55, 75, null, null, 231435775, 129417634, 178939153, 243302897, 538561, "ERX1065712", "ERS715221", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.20287, 0.52947, 0.14655, 0.13479, 0.96299, 0.93703, 0.56376, 0.52626, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13311, "ERR984490", "ERX1065711", "ERS715220", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367568", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367568|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 12 sc 2286392|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 12 sc 2286392|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#12", "13741619", "Illumina sequencing of library 13741619  constructed from sample accession ERS715220 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TGAACTGG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#12.cram", "cram", 746397730.0, 5741521.0, "SC RUN 16164 8#12", "0:55 1:75", "A:217959769;C:123138989;G:158254272;T:246531930;N:512770", 55, 75, null, null, 217959769, 123138989, 158254272, 246531930, 512770, "ERX1065711", "ERS715220", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.20695, 0.57674, 0.14123, 0.14978, 0.95899, 0.9138, 0.56705, 0.57522, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13312, "ERR984489", "ERX1065710", "ERS715219", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367567", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:01:26Z|External Id:SAMEA3367567|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:01:26Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 11 sc 2286391|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 11 sc 2286391|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#11", "13741618", "Illumina sequencing of library 13741618  constructed from sample accession ERS715219 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TTGGTATG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#11.cram", "cram", 630077890.0, 4846753.0, "SC RUN 16164 8#11", "0:55 1:75", "A:181555459;C:107913967;G:131155798;T:209016157;N:436509", 55, 75, null, null, 181555459, 107913967, 131155798, 209016157, 436509, "ERX1065710", "ERS715219", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.23034, 0.58664, 0.14994, 0.16031, 0.9517, 0.9134, 0.43491, 0.55537, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13313, "ERR984488", "ERX1065709", "ERS715218", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367566", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:57Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367566|INSDC center name:SC|INSDC first public:2015 08 18T09:04:57Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 10 sc 2286390|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 10 sc 2286390|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#10", "13741617", "Illumina sequencing of library 13741617  constructed from sample accession ERS715218 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TAACGCTG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#10.cram", "cram", 522425410.0, 4018657.0, "SC RUN 16164 8#10", "0:55 1:75", "A:136789388;C:88820863;G:131305976;T:165156817;N:352366", 55, 75, null, null, 136789388, 88820863, 131305976, 165156817, 352366, "ERX1065709", "ERS715218", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.16976, 0.61187, 0.10677, 0.16777, 0.96096, 0.93093, 0.59603, 0.58893, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13314, "ERR984487", "ERX1065708", "ERS715217", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367565", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367565|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 9 sc 2286389|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 9 sc 2286389|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#9", "13741616", "Illumina sequencing of library 13741616  constructed from sample accession ERS715217 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCGAAGTG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#9.cram", "cram", 662372100.0, 5095170.0, "SC RUN 16164 8#9", "0:55 1:75", "A:186346528;C:114321445;G:137139385;T:224106023;N:458719", 55, 75, null, null, 186346528, 114321445, 137139385, 224106023, 458719, "ERX1065708", "ERS715217", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.22854, 0.63729, 0.14734, 0.16003, 0.95089, 0.90751, 0.51773, 0.50977, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13315, "ERR984486", "ERX1065707", "ERS715216", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367564", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:55Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367564|INSDC center name:SC|INSDC first public:2015 08 18T09:04:55Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 8 sc 2286388|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 8 sc 2286388|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#8", "13741615", "Illumina sequencing of library 13741615  constructed from sample accession ERS715216 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TTCCATTG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#8.cram", "cram", 857007060.0, 6592362.0, "SC RUN 16164 8#8", "0:55 1:75", "A:257958701;C:131661477;G:190276240;T:276500331;N:610311", 55, 75, null, null, 257958701, 131661477, 190276240, 276500331, 610311, "ERX1065707", "ERS715216", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.21266, 0.595, 0.14225, 0.14037, 0.95964, 0.92232, 0.54595, 0.53111, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13316, "ERR984485", "ERX1065706", "ERS715215", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367563", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367563|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 7 sc 2286387|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 7 sc 2286387|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#7", "13741614", "Illumina sequencing of library 13741614  constructed from sample accession ERS715215 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TAGTCTTG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#7.cram", "cram", 742942590.0, 5714943.0, "SC RUN 16164 8#7", "0:55 1:75", "A:228799118;C:117009382;G:166056205;T:230565934;N:511951", 55, 75, null, null, 228799118, 117009382, 166056205, 230565934, 511951, "ERX1065706", "ERS715215", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.19264, 0.50767, 0.1428, 0.15173, 0.9666, 0.94606, 0.57413, 0.53902, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13317, "ERR984484", "ERX1065705", "ERS715214", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367562", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:40:24Z|External Id:SAMEA3367562|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:40:24Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 6 sc 2286386|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 6 sc 2286386|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#6", "13741613", "Illumina sequencing of library 13741613  constructed from sample accession ERS715214 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TGTGGTTG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#6.cram", "cram", 908951420.0, 6991934.0, "SC RUN 16164 8#6", "0:55 1:75", "A:266807632;C:158160652;G:194742499;T:288619707;N:620930", 55, 75, null, null, 266807632, 158160652, 194742499, 288619707, 620930, "ERX1065705", "ERS715214", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.20021, 0.52069, 0.13208, 0.1197, 0.95775, 0.93324, 0.52946, 0.52456, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13318, "ERR984483", "ERX1065704", "ERS715213", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367561", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367561|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 5 sc 2286385|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 5 sc 2286385|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#5", "13741612", "Illumina sequencing of library 13741612  constructed from sample accession ERS715213 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TCCTCAAT.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#5.cram", "cram", 771659330.0, 5935841.0, "SC RUN 16164 8#5", "0:55 1:75", "A:225161011;C:121434126;G:174639826;T:249876341;N:548026", 55, 75, null, null, 225161011, 121434126, 174639826, 249876341, 548026, "ERX1065704", "ERS715213", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.21069, 0.57513, 0.14228, 0.12501, 0.95672, 0.92488, 0.54397, 0.52111, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [13319, "ERR984482", "ERX1065703", "ERS715212", "ERP006132", "PRJEB6584", "Transcriptome profiling of embryos collected for one or more alleles identified by the zebrafish mutation project", "Transcriptome_profiling_of_embryos_collected_for_one_or_more_alleles_identified_by_the_zebrafish_mutation_project-sc-3191", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared for zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project for transcriptome profiling.", null, null, null, null, "SAMEA3367560", "SC", "ArrayExpress DevelopmentalStage:Segmentation:26+ somites ZFS:0000028   Pharyngula:Prim 5 ZFS:0000029|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2015 08 18T09:04:56Z|ENA LAST UPDATE:2018 03 09T00:00:47Z|External Id:SAMEA3367560|INSDC center name:SC|INSDC first public:2015 08 18T09:04:56Z|INSDC last update:2018 03 09T00:00:47Z|INSDC status:public|Submitter Id:ZMP phenotype 175 1 4 sc 2286384|common name:zebrafish|sample description:3 prime end enriched mRNA from a single embryo homozygous for pcna  allele sa8962 plus ERCC spike mix 1 Ambion. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/sanger/Zebrafish Zmpsearch/zmp ph175.|sample name:ZMP phenotype 175 1 4 sc 2286384|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 16164 8#4", "13741611", "Illumina sequencing of library 13741611  constructed from sample accession ERS715212 for study accession ERP006132.  This is part of an Illumina multiplexed sequencing run 16164 8.  This submission includes reads tagged with the sequence TACAGGAT.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP006132", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 18|ENA LAST UPDATE:2018 11 16", "16164_8#4.cram", "cram", 784183790.0, 6032183.0, "SC RUN 16164 8#4", "0:55 1:75", "A:219327080;C:128313123;G:169475262;T:266538585;N:529740", 55, 75, null, null, 219327080, 128313123, 169475262, 266538585, 529740, "ERX1065703", "ERS715212", "ERA466416", "The Wellcome Trust Sanger Institute|European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.20392, 0.58702, 0.12804, 0.12156, 0.96047, 0.9133, 0.61438, 0.53735, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-08-18", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"]], 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